chr2:29223441:G>A Detail (hg38) (ALK)

Information

Genome

Assembly Position
hg19 chr2:29,446,307-29,446,307 View the variant detail on this assembly version.
hg38 chr2:29,223,441-29,223,441

HGVS

Type Transcript Protein
RefSeq NM_004304.4:c.3260C>T NP_004295.2:p.Thr1087Ile
Ensemble ENST00000618119.4:c.2129C>T ENST00000618119.4:p.Thr710Ile
ENST00000389048.8:c.3260C>T ENST00000389048.8:p.Thr1087Ile
Summary

MGeND

Clinical significance Likely pathogenic
Variant entry 3
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.002
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 105590 OMIM
HGNC 427 HGNC
Ensembl ENSG00000171094 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6297881 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Likely pathogenic neuroblastoma germline MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
Likely pathogenic other germline MGS000001
(TMGS000162) 		Kenjiro Kosaki Keio University
Likely pathogenic other germline MGS000001
(TMGS000174) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Uncertain significance 2024-01-18 criteria provided, multiple submitters, no conflicts Neuroblastoma, susceptibility to, 3 germline unknown Detail
Uncertain significance 2023-06-21 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2022-01-01 criteria provided, single submitter ovarian cancer germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.240 Neuroblastoma, susceptibility to, 3 NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_004304.5(ALK):c.3260C>T (p.Thr1087Ile) AND Neuroblastoma, susceptibility to, 3 ClinVar Detail
NM_004304.5(ALK):c.3260C>T (p.Thr1087Ile) AND not provided ClinVar Detail
NM_004304.5(ALK):c.3260C>T (p.Thr1087Ile) AND Ovarian cancer ClinVar Detail
NA DisGeNET 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
rs113994090 dbSNP
Genome
hg38
Position
chr2:29,223,441-29,223,441
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
158.38
Standard deviation of sample read depth (HGVD)
71.12
Number of reference allele (HGVD)
2416
Number of alternative allele (HGVD)
4
Allele Frequency (HGVD)
0.001652892561983471
Gene Symbol (HGVD)
ALK
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs113994090
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0004
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
4
East Asian Heterozygous Counts (ExAC)
4
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
4.6221400508435407E-4
Chromosome Counts in All Race (ExAC)
121190
Allele Counts in All Race (ExAC)
4
Heterozygous Counts in All Race (ExAC)
4
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
3.300602359930687E-5
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