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NM_000350.3(ABCA4):c.6249C>T (p.Ile2083=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
10 (Most recent: Jan 7, 2021)
Last evaluated:
Nov 26, 2020
Accession:
VCV000099440.4
Variation ID:
99440
Description:
single nucleotide variant
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NM_000350.3(ABCA4):c.6249C>T (p.Ile2083=)

Allele ID
105329
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p22.1
Genomic location
1: 94001891 (GRCh38) GRCh38 UCSC
1: 94467447 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.94467447G>A
NC_000001.11:g.94001891G>A
NG_009073.1:g.124259C>T
NM_000350.3:c.6249C>T MANE Select NP_000341.2:p.Ile2083= synonymous
Protein change
-
Other names
p.I2083I:ATC>ATT
Canonical SPDI
NC_000001.11:94001890:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.13399 (A)

Allele frequency
1000 Genomes Project 0.13399
Trans-Omics for Precision Medicine (TOPMed) 0.13667
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.14601
The Genome Aggregation Database (gnomAD) 0.12420
Links
ClinGen: CA202924
dbSNP: rs1801359
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 Aug 25, 2014 RCV000178562.2
Benign 2 criteria provided, single submitter Nov 26, 2020 RCV000085799.4
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000289405.2
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000329139.2
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000344433.2
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000383722.2
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV001101662.1
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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
2111 2141

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Jul 05, 2011)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000166756.10
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
(Aug 25, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000230666.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000303775.1
Submitted: (Apr 28, 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: SCV000359220.2
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: SCV000359222.2
Submitted: (Oct 18, 2016)
Evidence details
Publications
PubMed (1)
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Stargardt Disease, Recessive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000359219.2
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: SCV000359221.2
Submitted: (Oct 18, 2016)
Evidence details
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
ABCA4-Related Disorders
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001258288.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Nov 26, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001718112.1
Submitted: (Jan 07, 2021)
Evidence details
not provided
(-)
no assertion provided
Method: not provided
not provided
Allele origin: not provided
Retina International
Accession: SCV000117942.1
Submitted: (Dec 20, 2012)
Comment:
http://phencode.bx.psu.edu/cgi-bin/phencode/phencode?build=hg19&id=RISN_ABCR:c.6249C>T
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
ABCA4 mutations in Portuguese Stargardt patients: identification of new mutations and their phenotypic analysis. Maia-Lopes S Molecular vision 2009 PMID: 19365591
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ABCA4 - - - -

Text-mined citations for rs1801359...

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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 Nov 20, 2021