NM_005751.4(AKAP9):c.10331A>G (p.Gln3444Arg) AND not specified

Clinical significance:Benign (Last evaluated: Oct 15, 2019)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000171783.2

Allele description [Variation Report for NM_005751.4(AKAP9):c.10331A>G (p.Gln3444Arg)]

NM_005751.4(AKAP9):c.10331A>G (p.Gln3444Arg)

Gene:
AKAP9:A-kinase anchoring protein 9 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q21.2
Genomic location:
Preferred name:
NM_005751.4(AKAP9):c.10331A>G (p.Gln3444Arg)
HGVS:
  • NC_000007.14:g.92097290A>G
  • NG_011623.1:g.161416A>G
  • NM_005751.4:c.10331A>G
  • NM_147185.3:c.10307A>G
  • NP_005742.4:p.Gln3444Arg
  • NP_671714.1:p.Gln3436Arg
  • LRG_331t1:c.10331A>G
  • LRG_331:g.161416A>G
  • LRG_331p1:p.Gln3444Arg
  • NC_000007.13:g.91726604A>G
Protein change:
Q3436R
Links:
dbSNP: rs34956633
NCBI 1000 Genomes Browser:
rs34956633
Molecular consequence:
  • NM_005751.4:c.10331A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_147185.3:c.10307A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000055241Biesecker Lab/Clinical Genomics Section,National Institutes of Health - ClinSeqcriteria provided, single submitter
Benign
(Jun 24, 2013)
unknownresearch

PubMed (1)
[See all records that cite this PMID]

SCV001361463Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(Oct 15, 2019)
germlineclinical testing

Citation Link

Description

The study set was not selected for affection status in relation to any cancer. Pathogenicity categories were based on literature curation. See Pubmed ID:23861362 for details.

SCV000055241

Medical sequencing

SCV000055241

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknown2not providednot providednot providednot providedresearch

Citations

PubMed

Interpreting secondary cardiac disease variants in an exome cohort.

Ng D, Johnston JJ, Teer JK, Singh LN, Peller LC, Wynter JS, Lewis KL, Cooper DN, Stenson PD, Mullikin JC, Biesecker LG; NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program..

Circ Cardiovasc Genet. 2013 Aug;6(4):337-46. doi: 10.1161/CIRCGENETICS.113.000039. Epub 2013 Jul 16.

PubMed [citation]
PMID:
23861362
PMCID:
PMC3887521

Details of each submission

From Biesecker Lab/Clinical Genomics Section,National Institutes of Health - ClinSeq, SCV000055241.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedresearch PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot provided2not providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001361463.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: AKAP9 c.10331A>G (p.Gln3444Arg) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0037 in 246960 control chromosomes, predominantly at a frequency of 0.049 within the African or African-American subpopulation in the gnomAD database, including 23 homozygotes. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 4900-folds of the estimated maximal expected allele frequency for a pathogenic variant in AKAP9 causing Arrhythmia phenotype (1e-05), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. Three ClinVar submissions (evaluation after 2014) cites the variant twice as benign and once as likely benign. Based on the evidence outlined above, the variant was classified as benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2021

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