chr3:10064848:C>T Detail (hg38) (FANCD2, LOC107303338)

Information

Genome

Assembly Position
hg19 chr3:10,106,532-10,106,532 View the variant detail on this assembly version.
hg38 chr3:10,064,848-10,064,848

HGVS

Type Transcript Protein
RefSeq NM_033084.4:c.2141C>T NP_149075.2:p.Pro714Leu
NM_001319984.1:c.2141C>T NP_001306913.1:p.Pro714Leu
Ensemble ENST00000287647.7:c.2141C>T ENST00000287647.7:p.Pro714Leu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.033
ToMMo:0.048
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.059

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 613984 OMIM
HGNC 3585 HGNC
Ensembl ENSG00000144554 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv11437317 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2021-12-03 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts Fanconi anemia germline Detail
Benign 2019-05-28 criteria provided, single submitter Fanconi anemia complementation group A unknown Detail
Benign 2023-07-07 criteria provided, multiple submitters, no conflicts Fanconi anemia complementation group D2 germline Detail
Benign 2019-03-01 criteria provided, single submitter not provided germline Detail
Benign 2022-04-19 criteria provided, single submitter hereditary breast ovarian cancer syndrome germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_001018115.3(FANCD2):c.2141C>T (p.Pro714Leu) AND not specified ClinVar Detail
NM_001018115.3(FANCD2):c.2141C>T (p.Pro714Leu) AND Fanconi anemia ClinVar Detail
NM_001018115.3(FANCD2):c.2141C>T (p.Pro714Leu) AND Fanconi anemia complementation group A ClinVar Detail
NM_001018115.3(FANCD2):c.2141C>T (p.Pro714Leu) AND Fanconi anemia complementation group D2 ClinVar Detail
NM_001018115.3(FANCD2):c.2141C>T (p.Pro714Leu) AND not provided ClinVar Detail
NM_001018115.3(FANCD2):c.2141C>T (p.Pro714Leu) AND Hereditary breast ovarian cancer syndrome ClinVar Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs3864017 dbSNP
Genome
hg38
Position
chr3:10,064,848-10,064,848
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
VQSRTrancheSNP99.00to99.90
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
837
Mean of sample read depth (HGVD)
16.13
Standard deviation of sample read depth (HGVD)
46.78
Number of reference allele (HGVD)
1618
Number of alternative allele (HGVD)
56
Allele Frequency (HGVD)
0.03345280764635603
Gene Symbol (HGVD)
FANCD2
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
VQSRTrancheSNP99.80to99.90
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs3864017
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0483
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
809
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8592
East Asian Allele Counts (ExAC)
505
East Asian Heterozygous Counts (ExAC)
497
East Asian Homozygous Counts (ExAC)
4
East Asian Allele Frequency (ExAC)
0.0587756052141527
Chromosome Counts in All Race (ExAC)
120684
Allele Counts in All Race (ExAC)
18644
Heterozygous Counts in All Race (ExAC)
16668
Homozygous Counts in All Race (ExAC)
988
Allele Frequency in All Race (ExAC)
0.1544860959199231
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