chr11-19186294-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001369404.1(CSRP3):c.167G>A(p.Arg56Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0934 in 1,614,124 control chromosomes in the GnomAD database, including 7,823 homozygotes. In-silico tool predicts a benign outcome for this variant. 7/9 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001369404.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0719 AC: 10946AN: 152150Hom.: 543 Cov.: 32
GnomAD3 exomes AF: 0.0798 AC: 20048AN: 251352Hom.: 1053 AF XY: 0.0825 AC XY: 11203AN XY: 135834
GnomAD4 exome AF: 0.0956 AC: 139749AN: 1461856Hom.: 7278 Cov.: 33 AF XY: 0.0953 AC XY: 69293AN XY: 727232
GnomAD4 genome AF: 0.0719 AC: 10945AN: 152268Hom.: 545 Cov.: 32 AF XY: 0.0710 AC XY: 5284AN XY: 74432
ClinVar
Submissions by phenotype
not specified Benign:8
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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 a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not provided Uncertain:1Benign:2
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Allele frequency is common in at least one population database (frequency: 11.585% in ExAC) based on the frequency threshold of 5.0% for this gene. Variant was observed in a homozygous state in population databases more than expected for disease. 1 reputable source/s reports the variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation. A synonymous variant not located in a splice region. -
Primary dilated cardiomyopathy Pathogenic:1
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Hypertrophic cardiomyopathy 12 Benign:1
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 by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Cardiomyopathy Benign:1
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Dilated cardiomyopathy 1M;C2677491:Hypertrophic cardiomyopathy 12 Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as 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