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NM_001378454.1(ALMS1):c.2658A>G (p.Lys886=) AND not specified

Germline classification:
Benign (1 submission)
Last evaluated:
Jul 30, 2018
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000430379.5

Allele description [Variation Report for NM_001378454.1(ALMS1):c.2658A>G (p.Lys886=)]

NM_001378454.1(ALMS1):c.2658A>G (p.Lys886=)

Gene:
ALMS1:ALMS1 centrosome and basal body associated protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p13.1
Genomic location:
Preferred name:
NM_001378454.1(ALMS1):c.2658A>G (p.Lys886=)
HGVS:
  • NC_000002.12:g.73449185A>G
  • NG_011690.1:g.68433A>G
  • NM_001378454.1:c.2658A>GMANE SELECT
  • NM_015120.4:c.2661A>G
  • NP_001365383.1:p.Lys886=
  • NP_055935.4:p.Lys887=
  • LRG_741t1:c.2661A>G
  • LRG_741:g.68433A>G
  • LRG_741p1:p.Lys887=
  • NC_000002.11:g.73676312A>G
Links:
dbSNP: rs80133984
NCBI 1000 Genomes Browser:
rs80133984
Molecular consequence:
  • NM_001378454.1:c.2658A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_015120.4:c.2661A>G - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV000864087Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Benign
(Jul 30, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000864087.2

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

Description

Variant summary: ALMS1 c.2655A>G (alternative c.2661A>G) alters a non-conserved nucleotide resulting in a synonymous change. The variant allele was found at a frequency of 0.00081 in 276666 control chromosomes, and was predominantly within the African subpopulation in the gnomAD database at a frequency of 0.0084, including 2 homozygotes. The observed variant frequency within African control individuals is approximately 3.8-fold above the estimated maximal expected allele frequency for a pathogenic variant in ALMS1 causing Cardiomyopathy phenotype (0.0022), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. To our knowledge, no occurrence of c.2655A>G in individuals affected with Cardiomyopathy and no experimental evidence demonstrating its impact on protein function have been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and both classified the variant as benign/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, 2024