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NM_000350.3(ABCA4):c.1653G>A (p.Val551=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(2);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 24, 2020
Accession:
VCV000099071.5
Variation ID:
99071
Description:
single nucleotide variant
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NM_000350.3(ABCA4):c.1653G>A (p.Val551=)

Allele ID
104960
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p22.1
Genomic location
1: 94063219 (GRCh38) GRCh38 UCSC
1: 94528775 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.94528775C>T
NC_000001.11:g.94063219C>T
NM_000350.3:c.1653G>A MANE Select NP_000341.2:p.Val551= synonymous
NG_009073.1:g.62931G>A
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:94063218:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00160 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00274
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00300
1000 Genomes Project 0.00160
Trans-Omics for Precision Medicine (TOPMed) 0.00242
Exome Aggregation Consortium (ExAC) 0.00067
The Genome Aggregation Database (gnomAD), exomes 0.00054
Links
ClinGen: CA200895
dbSNP: rs61753963
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts May 31, 2017 RCV000174240.2
Benign 2 criteria provided, single submitter Nov 24, 2020 RCV000085414.4
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV001100051.1
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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
1992 2022

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(May 31, 2017)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000719688.1
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)
Likely benign
(Jun 03, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000225509.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
ABCA4-Related Disorders
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001256552.1
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
(Nov 24, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001023451.3
Submitted: (Jan 07, 2021)
Evidence details
not provided
(-)
no assertion provided
Method: not provided
not provided
Allele origin: not provided
Retina International
Accession: SCV000117551.1
Submitted: (Dec 20, 2012)
Comment:
http://phencode.bx.psu.edu/cgi-bin/phencode/phencode?build=hg19&id=RISN_ABCR:c.1653G>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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ABCA4 - - - -

Text-mined citations for rs61753963...

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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 Jun 14, 2021