rs372152495
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 2P and 14B. PM2BP4_ModerateBP6_Very_StrongBS1
The NM_000337.6(SGCD):āc.144G>Cā(p.Val48Val) variant causes a synonymous change. The variant allele was found at a frequency of 0.000172 in 1,611,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_000337.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SGCD | ENST00000337851.9 | c.144G>C | p.Val48Val | synonymous_variant | Exon 3 of 9 | 1 | NM_000337.6 | ENSP00000338343.4 | ||
SGCD | ENST00000435422.7 | c.141G>C | p.Val47Val | synonymous_variant | Exon 2 of 8 | 1 | ENSP00000403003.2 | |||
SGCD | ENST00000517913.5 | c.144G>C | p.Val48Val | synonymous_variant | Exon 5 of 10 | 5 | ENSP00000429378.1 | |||
SGCD | ENST00000524347.2 | n.144G>C | non_coding_transcript_exon_variant | Exon 3 of 6 | 5 | ENSP00000430794.1 |
Frequencies
GnomAD3 genomes AF: 0.000934 AC: 142AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000182 AC: 45AN: 246876Hom.: 0 AF XY: 0.000149 AC XY: 20AN XY: 133974
GnomAD4 exome AF: 0.0000932 AC: 136AN: 1459650Hom.: 0 Cov.: 32 AF XY: 0.0000882 AC XY: 64AN XY: 726034
GnomAD4 genome AF: 0.000933 AC: 142AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.000994 AC XY: 74AN XY: 74428
ClinVar
Submissions by phenotype
not specified Benign:5
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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. -
proposed classification - variant undergoing re-assessment, contact laboratory -
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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 likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
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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Dilated cardiomyopathy 1L Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at