chr1:94001068:C>T Detail (hg38) (ABCA4)

Information

Genome

Assembly Position
hg19 chr1:94,466,624-94,466,624 View the variant detail on this assembly version.
hg38 chr1:94,001,068-94,001,068

HGVS

Type Transcript Protein
RefSeq NM_000350.2:c.6320G>A NP_000341.2:p.Arg2107His
Ensemble ENST00000370225.4:c.6320G>A ENST00000370225.4:p.Arg2107His
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.002
ToMMo:0.004
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 601691 OMIM
HGNC 34 HGNC
Ensembl ENSG00000198691 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv2419833 TogoVar
COSMIC COSM913440 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic Likely pathogenic 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline not provided Detail
Conflicting interpretations of pathogenicity 2024-03-26 criteria provided, conflicting interpretations Severe early-childhood-onset retinal dystrophy germline unknown Detail
Likely pathogenic 2015-01-01 no assertion criteria provided unknown Detail
Pathogenic 2023-10-01 criteria provided, multiple submitters, no conflicts Retinal dystrophy germline Detail
Likely pathogenic 2021-01-30 criteria provided, single submitter Severe early-childhood-onset retinal dystrophy germline Detail
Likely pathogenic 2023-10-02 criteria provided, single submitter Stargardt disease germline Detail
Likely pathogenic 2023-03-12 criteria provided, single submitter ABCA4-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.442 STARGARDT DISEASE 1 (disorder) Twenty-nine patients with Stargardt dystrophy or fundus flavimaculatus from diff... UNIPROT 10206579 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000350.3(ABCA4):c.6320G>A (p.Arg2107His) AND not provided ClinVar Detail
NM_000350.3(ABCA4):c.6320G>A (p.Arg2107His) AND Severe early-childhood-onset retinal dystrophy ClinVar Detail
NM_000350.3(ABCA4):c.6320G>A (p.Arg2107His) AND Macular dystrophy ClinVar Detail
NM_000350.3(ABCA4):c.6320G>A (p.Arg2107His) AND Retinal dystrophy ClinVar Detail
NM_000350.3(ABCA4):c.[3322C>T;6320G>A] AND Severe early-childhood-onset retinal dystrophy ClinVar Detail
NM_000350.3(ABCA4):c.6320G>A (p.Arg2107His) AND Stargardt disease ClinVar Detail
NM_000350.3(ABCA4):c.6320G>A (p.Arg2107His) AND ABCA4-related disorder ClinVar Detail
Twenty-nine patients with Stargardt dystrophy or fundus flavimaculatus from different pedigrees were... 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
rs62642564 dbSNP
Genome
hg38
Position
chr1:94,001,068-94,001,068
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1200
Mean of sample read depth (HGVD)
46.82
Standard deviation of sample read depth (HGVD)
22.90
Number of reference allele (HGVD)
2396
Number of alternative allele (HGVD)
4
Allele Frequency (HGVD)
0.0016666666666666668
Gene Symbol (HGVD)
ABCA4
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))
rs62642564
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0042
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
71
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8640
East Asian Allele Counts (ExAC)
10
East Asian Heterozygous Counts (ExAC)
8
East Asian Homozygous Counts (ExAC)
1
East Asian Allele Frequency (ExAC)
0.0011574074074074073
Chromosome Counts in All Race (ExAC)
121250
Allele Counts in All Race (ExAC)
227
Heterozygous Counts in All Race (ExAC)
221
Homozygous Counts in All Race (ExAC)
3
Allele Frequency in All Race (ExAC)
0.0018721649484536083
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