rs45559835
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000337.6(SGCD):c.290G>A(p.Arg97Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0543 in 1,568,098 control chromosomes in the GnomAD database, including 2,622 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000337.6 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: 0.0420 AC: 6393AN: 152062Hom.: 188 Cov.: 32
GnomAD3 exomes AF: 0.0453 AC: 10602AN: 234230Hom.: 292 AF XY: 0.0454 AC XY: 5760AN XY: 126922
GnomAD4 exome AF: 0.0557 AC: 78825AN: 1415918Hom.: 2435 Cov.: 24 AF XY: 0.0549 AC XY: 38702AN XY: 705496
GnomAD4 genome AF: 0.0420 AC: 6389AN: 152180Hom.: 187 Cov.: 32 AF XY: 0.0409 AC XY: 3044AN XY: 74400
ClinVar
Submissions by phenotype
not specified Benign:8
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Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
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not provided Benign:4
This variant is associated with the following publications: (PMID: 10974018, 26968544, 28401079) -
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Autosomal recessive limb-girdle muscular dystrophy type 2F Benign:3
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Limb-girdle muscular dystrophy, recessive Benign:1
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Qualitative or quantitative defects of delta-sarcoglycan 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. -
Cardiovascular phenotype Benign:1
This alteration is classified as benign based on a combination of the following: 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. -
Dilated cardiomyopathy 1L Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at