chr1:94496053:G>A Detail (hg19) (ABCA4)

Information

Genome

Assembly Position
hg19 chr1:94,496,053-94,496,053
hg38 chr1:94,030,497-94,030,497 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000350.2:c.4283C>T NP_000341.2:p.Thr1428Met
Ensemble ENST00000370225.4:c.4283C>T ENST00000370225.4:p.Thr1428Met
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.035
ToMMo:0.037
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.052

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 tgv2421426 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline not provided Detail
Benign 2014-06-09 criteria provided, single submitter not specified germline Detail
Likely benign 2016-06-14 criteria provided, single submitter Cone-Rod Dystrophy, 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 Retinitis Pigmentosa, Recessive germline Detail
Likely benign 2016-06-14 criteria provided, single submitter macular degeneration 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
0.360 Macular Degeneration, Age-Related, 2 NA UNIPROT Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000350.3(ABCA4):c.4283C>T (p.Thr1428Met) AND not provided ClinVar Detail
NM_000350.3(ABCA4):c.4283C>T (p.Thr1428Met) AND not specified ClinVar Detail
NM_000350.3(ABCA4):c.4283C>T (p.Thr1428Met) AND Cone-Rod Dystrophy, Recessive ClinVar Detail
NM_000350.3(ABCA4):c.4283C>T (p.Thr1428Met) AND Stargardt Disease, Recessive ClinVar Detail
NM_000350.3(ABCA4):c.4283C>T (p.Thr1428Met) AND Retinitis Pigmentosa, Recessive ClinVar Detail
NM_000350.3(ABCA4):c.4283C>T (p.Thr1428Met) AND Macular degeneration ClinVar Detail
NM_000350.3(ABCA4):c.4283C>T (p.Thr1428Met) AND ABCA4-related disorder ClinVar Detail
NM_000350.3(ABCA4):c.4283C>T (p.Thr1428Met) AND Retinal dystrophy 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
rs1800549 dbSNP
Genome
hg19
Position
chr1:94,496,053-94,496,053
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1204
Mean of sample read depth (HGVD)
54.91
Standard deviation of sample read depth (HGVD)
26.85
Number of reference allele (HGVD)
2324
Number of alternative allele (HGVD)
84
Allele Frequency (HGVD)
0.03488372093023256
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))
rs1800549
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0374
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
627
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8644
East Asian Allele Counts (ExAC)
447
East Asian Heterozygous Counts (ExAC)
423
East Asian Homozygous Counts (ExAC)
12
East Asian Allele Frequency (ExAC)
0.051712170291531696
Chromosome Counts in All Race (ExAC)
121376
Allele Counts in All Race (ExAC)
500
Heterozygous Counts in All Race (ExAC)
476
Homozygous Counts in All Race (ExAC)
12
Allele Frequency in All Race (ExAC)
0.004119430529923544
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