rs10071079
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000337.6(SGCD):c.507G>A(p.Ala169Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00121 in 1,580,166 control chromosomes in the GnomAD database, including 21 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 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SGCD | ENST00000337851.9 | c.507G>A | p.Ala169Ala | synonymous_variant | Exon 7 of 9 | 1 | NM_000337.6 | ENSP00000338343.4 | ||
SGCD | ENST00000435422.7 | c.504G>A | p.Ala168Ala | synonymous_variant | Exon 6 of 8 | 1 | ENSP00000403003.2 | |||
SGCD | ENST00000517913.5 | c.507G>A | p.Ala169Ala | synonymous_variant | Exon 9 of 10 | 5 | ENSP00000429378.1 |
Frequencies
GnomAD3 genomes AF: 0.00628 AC: 955AN: 152100Hom.: 11 Cov.: 33
GnomAD3 exomes AF: 0.00139 AC: 284AN: 204028Hom.: 3 AF XY: 0.00117 AC XY: 128AN XY: 108992
GnomAD4 exome AF: 0.000672 AC: 960AN: 1427948Hom.: 10 Cov.: 29 AF XY: 0.000574 AC XY: 406AN XY: 707038
GnomAD4 genome AF: 0.00628 AC: 956AN: 152218Hom.: 11 Cov.: 33 AF XY: 0.00591 AC XY: 440AN XY: 74398
ClinVar
Submissions by phenotype
not specified Benign:3
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1.5% (59/3856) of Afr Amer chrom from ESP -
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not provided Benign:3
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Autosomal recessive limb-girdle muscular dystrophy type 2F Benign:2
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SGCD-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
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. -
Limb-girdle muscular dystrophy, recessive Benign:1
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Inborn genetic diseases 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. -
Cardiomyopathy Benign:1
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Autosomal recessive limb-girdle muscular dystrophy type 2F;C1847667:Dilated cardiomyopathy 1L Benign:1
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Dilated cardiomyopathy 1L Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at