chr13-23203702-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_000231.3(SGCG):c.8G>A(p.Arg3His) variant causes a missense change. The variant allele was found at a frequency of 0.0000651 in 1,611,892 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R3C) has been classified as Uncertain significance.
Frequency
Consequence
NM_000231.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SGCG | NM_000231.3 | c.8G>A | p.Arg3His | missense_variant | 2/8 | ENST00000218867.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGCG | ENST00000218867.4 | c.8G>A | p.Arg3His | missense_variant | 2/8 | 1 | NM_000231.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000289 AC: 44AN: 152136Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.0000766 AC: 19AN: 248066Hom.: 0 AF XY: 0.0000747 AC XY: 10AN XY: 133946
GnomAD4 exome AF: 0.0000377 AC: 55AN: 1459638Hom.: 0 Cov.: 31 AF XY: 0.0000386 AC XY: 28AN XY: 725930
GnomAD4 genome ? AF: 0.000328 AC: 50AN: 152254Hom.: 1 Cov.: 33 AF XY: 0.000336 AC XY: 25AN XY: 74444
ClinVar
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2C Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2022 | This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 3 of the SGCG protein (p.Arg3His). This variant is present in population databases (rs35105771, gnomAD 0.06%). This variant has not been reported in the literature in individuals affected with SGCG-related conditions. ClinVar contains an entry for this variant (Variation ID: 284971). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jun 30, 2021 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 04, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at