rs774582375
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_000231.3(SGCG):c.506-7T>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,611,580 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000231.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SGCG | ENST00000218867.4 | c.506-7T>G | splice_region_variant, intron_variant | Intron 5 of 7 | 1 | NM_000231.3 | ENSP00000218867.3 | |||
SACS | ENST00000683210.1 | c.2186-6165A>C | intron_variant | Intron 9 of 9 | ENSP00000506739.1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000994 AC: 25AN: 251430Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135892
GnomAD4 exome AF: 0.000116 AC: 170AN: 1459388Hom.: 2 Cov.: 29 AF XY: 0.000127 AC XY: 92AN XY: 726300
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74362
ClinVar
Submissions by phenotype
not provided Uncertain:2
SGCG: PM2, BP4 -
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Autosomal recessive limb-girdle muscular dystrophy type 2C Uncertain:1Benign:1
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not specified Benign:1
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at