chr1:215807920:A>G Detail (hg19) (USH2A)

Information

Genome

Assembly Position
hg19 chr1:215,807,920-215,807,920
hg38 chr1:215,634,578-215,634,578 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_206933.2:c.15178T>C NP_996816.2:p.Ser5060Pro
Ensemble ENST00000307340.8:c.15178T>C ENST00000307340.8:p.Ser5060Pro
ENST00000674083.1:c.15178T>C ENST00000674083.1:p.Ser5060Pro
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
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 608400 OMIM
HGNC 12601 HGNC
Ensembl ENSG00000042781 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv4773253 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Uncertain significance 2017-05-22 criteria provided, single submitter retinitis pigmentosa 39,Usher syndrome type 2A unknown Detail
Uncertain significance 2017-05-22 criteria provided, single submitter retinitis pigmentosa 39,Usher syndrome type 2A unknown Detail
Pathogenic criteria provided, single submitter Usher syndrome type 2A germline Detail
Pathogenic 2024-01-24 criteria provided, single submitter not provided germline Detail
Uncertain significance 2023-10-01 criteria provided, multiple submitters, no conflicts Retinal dystrophy germline Detail
Likely pathogenic 2023-10-20 criteria provided, single submitter retinitis pigmentosa 39 unknown Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_206933.4(USH2A):c.15178T>C (p.Ser5060Pro) AND multiple conditions ClinVar Detail
NM_206933.4(USH2A):c.15178T>C (p.Ser5060Pro) AND multiple conditions ClinVar Detail
NM_206933.4(USH2A):c.15178T>C (p.Ser5060Pro) AND Usher syndrome type 2A ClinVar Detail
NM_206933.4(USH2A):c.15178T>C (p.Ser5060Pro) AND not provided ClinVar Detail
NM_206933.4(USH2A):c.15178T>C (p.Ser5060Pro) AND Retinal dystrophy ClinVar Detail
NM_206933.4(USH2A):c.15178T>C (p.Ser5060Pro) AND Retinitis pigmentosa 39 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
rs752377040 dbSNP
Genome
hg19
Position
chr1:215,807,920-215,807,920
Variant Type
snv
Reference Allele
A
Alternative Allele
G
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))
rs752377040
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0002
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4
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)
121412
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)
3.2945672585905844E-5
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