12-21814684-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS1
The NM_020297.4(ABCC9):c.4062G>A(p.Ser1354Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000118 in 1,613,818 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_020297.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152072Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000916 AC: 23AN: 251150Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135704
GnomAD4 exome AF: 0.000112 AC: 164AN: 1461746Hom.: 1 Cov.: 31 AF XY: 0.000125 AC XY: 91AN XY: 727172
GnomAD4 genome AF: 0.000171 AC: 26AN: 152072Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74264
ClinVar
Submissions by phenotype
not provided Benign:6
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ABCC9: BP4, BP7 -
not specified Benign:2
Ser1354Ser in exon 33 of ABCC9: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. It has been identified in 1/8600 European A merican chromosomes and 1/4406 African American chromosomes from a broad populat ion by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS/; db SNP rs145005748). Ser1354Ser in exon 33 of ABCC9 (rs145005748; allele frequency = 1/8600) ** -
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Dilated cardiomyopathy 1O Benign:1
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Cardiomyopathy Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at