chr1:94544234:T>C Detail (hg19) (ABCA4)

Information

Genome

Assembly Position
hg19 chr1:94,544,234-94,544,234
hg38 chr1:94,078,678-94,078,678 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000350.2:c.1268A>G NP_000341.2:p.His423Arg
Ensemble ENST00000370225.4:c.1268A>G ENST00000370225.4:p.His423Arg
ENST00000649773.1:c.1268A>G ENST00000649773.1:p.His423Arg
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.263
ToMMo:0.262
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.248

Prediction

ClinVar

Clinical Significance Benign Likely benign
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 tgv2423528 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline not provided Detail
Benign 2014-05-19 criteria provided, multiple submitters, no conflicts not specified germline Detail
Likely benign 2016-06-14 criteria provided, single submitter macular degeneration germline Detail
Likely benign 2016-06-14 criteria provided, single submitter Retinitis Pigmentosa, Recessive germline Detail
Likely benign 2016-06-14 criteria provided, single submitter Stargardt Disease, Recessive germline Detail
Likely benign 2016-06-14 criteria provided, single submitter Cone-Rod Dystrophy, Recessive germline Detail
Likely benign 2017-04-27 criteria provided, single submitter ABCA4-related disorder germline Detail
Benign 2023-10-01 criteria provided, single submitter Retinal dystrophy germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 age related macular degeneration A variant located at the 3' UTR of the FGF2 gene (rs6820411) was highly associat... BeFree 21106043 Detail
<0.001 Atrophic condition of skin A variant located at the 3' UTR of the FGF2 gene (rs6820411) was highly associat... BeFree 21106043 Detail
<0.001 Atrophic condition of skin A variant located at the 3' UTR of the FGF2 gene (rs6820411) was highly associat... BeFree 21106043 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000350.3(ABCA4):c.1268A>G (p.His423Arg) AND not provided ClinVar Detail
NM_000350.3(ABCA4):c.1268A>G (p.His423Arg) AND not specified ClinVar Detail
NM_000350.3(ABCA4):c.1268A>G (p.His423Arg) AND Macular degeneration ClinVar Detail
NM_000350.3(ABCA4):c.1268A>G (p.His423Arg) AND Retinitis Pigmentosa, Recessive ClinVar Detail
NM_000350.3(ABCA4):c.1268A>G (p.His423Arg) AND Stargardt Disease, Recessive ClinVar Detail
NM_000350.3(ABCA4):c.1268A>G (p.His423Arg) AND Cone-Rod Dystrophy, Recessive ClinVar Detail
NM_000350.3(ABCA4):c.1268A>G (p.His423Arg) AND ABCA4-related disorder ClinVar Detail
NM_000350.3(ABCA4):c.1268A>G (p.His423Arg) AND Retinal dystrophy ClinVar Detail
A variant located at the 3' UTR of the FGF2 gene (rs6820411) was highly associated with atrophic AMD... DisGeNET Detail
A variant located at the 3' UTR of the FGF2 gene (rs6820411) was highly associated with atrophic AMD... DisGeNET Detail
A variant located at the 3' UTR of the FGF2 gene (rs6820411) was highly associated with atrophic AMD... 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
rs3112831 dbSNP
Genome
hg19
Position
chr1:94,544,234-94,544,234
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
146.24
Standard deviation of sample read depth (HGVD)
71.55
Number of reference allele (HGVD)
1784
Number of alternative allele (HGVD)
636
Allele Frequency (HGVD)
0.2628099173553719
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))
rs3112831
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2621
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4392
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8646
East Asian Allele Counts (ExAC)
2142
East Asian Heterozygous Counts (ExAC)
1610
East Asian Homozygous Counts (ExAC)
266
East Asian Allele Frequency (ExAC)
0.2477446217904233
Chromosome Counts in All Race (ExAC)
121400
Allele Counts in All Race (ExAC)
30988
Heterozygous Counts in All Race (ExAC)
22478
Homozygous Counts in All Race (ExAC)
4255
Allele Frequency in All Race (ExAC)
0.2552553542009885
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