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NM_000350.3(ABCA4):c.6732G>A (p.Val2244=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(4);Likely benign(5);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
11 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 5, 2020
Accession:
VCV000099492.5
Variation ID:
99492
Description:
single nucleotide variant
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NM_000350.3(ABCA4):c.6732G>A (p.Val2244=)

Allele ID
105381
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p22.1
Genomic location
1: 93996193 (GRCh38) GRCh38 UCSC
1: 94461749 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.94461749C>T
NC_000001.11:g.93996193C>T
NG_009073.1:g.129957G>A
NM_000350.3:c.6732G>A MANE Select NP_000341.2:p.Val2244= synonymous
Protein change
-
Other names
p.V2244V:GTG>GTA
Canonical SPDI
NC_000001.11:93996192:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.02915 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00650
Exome Aggregation Consortium (ExAC) 0.00796
1000 Genomes Project 0.02915
The Genome Aggregation Database (gnomAD) 0.02401
Trans-Omics for Precision Medicine (TOPMed) 0.02584
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.02591
Links
ClinGen: CA285827
dbSNP: rs77293072
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Jun 11, 2015 RCV000211883.3
Benign 2 criteria provided, single submitter Dec 5, 2020 RCV000085853.6
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000315445.1
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000351693.1
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000390572.1
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000407170.1
Uncertain significance 1 criteria provided, single submitter Jan 1, 2016 RCV000408548.1
Likely benign 1 criteria provided, single submitter Jan 12, 2018 RCV001097883.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ABCA4 - - GRCh38
GRCh37
2037 2067

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jul 18, 2011)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000166760.10
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000303783.1
Submitted: (Apr 28, 2016)
Evidence details
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Stargardt Disease, Recessive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000359186.2
Submitted: (Oct 18, 2016)
Evidence details
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Retinitis Pigmentosa, Recessive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000359183.2
Submitted: (Oct 18, 2016)
Evidence details
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Macular Degeneration
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000359185.2
Submitted: (Oct 18, 2016)
Evidence details
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Cone-Rod Dystrophy, Recessive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000359184.2
Submitted: (Oct 18, 2016)
Evidence details
Uncertain significance
(Jan 01, 2016)
criteria provided, single submitter
Method: clinical testing
Stargardt disease 1
Allele origin: germline
Institute of Human Genetics, Univ. Regensburg,Univ. Regensburg
Accession: SCV000281965.2
Submitted: (May 25, 2016)
Evidence details
Publications
PubMed (3)
Benign
(Jun 11, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000332063.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
http://www.ncbi.nlm.nih.gov/vari…
Likely benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
ABCA4-Related Disorders
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001254209.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001102456.3
Submitted: (Jan 07, 2021)
Evidence details
not provided
(-)
no assertion provided
Method: not provided
not provided
Allele origin: not provided
Retina International
Accession: SCV000117996.1
Submitted: (Dec 20, 2012)
Comment:
http://phencode.bx.psu.edu/cgi-bin/phencode/phencode?build=hg19&id=RISN_ABCR:c.6732G>A
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Mutation Spectrum of the ABCA4 Gene in 335 Stargardt Disease Patients From a Multicenter German Cohort-Impact of Selected Deep Intronic Variants and Common SNPs. Schulz HL Investigative ophthalmology & visual science 2017 PMID: 28118664
Detection rate of pathogenic mutations in ABCA4 using direct sequencing: clinical and research implications. Downes SM Archives of ophthalmology (Chicago, Ill. : 1960) 2012 PMID: 23143460
Analysis of the ABCA4 gene by next-generation sequencing. Zernant J Investigative ophthalmology & visual science 2011 PMID: 21911583
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ABCA4 - - - -
http://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/?chr=1&from=94461749&to=94461749 - - - -

Text-mined citations for rs77293072...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 07, 2021