1-930164-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001385641.1(SAMD11):c.619C>T(p.Arg207Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000109 in 1,556,398 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R207Q) has been classified as Benign.
Frequency
Consequence
NM_001385641.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SAMD11 | NM_001385641.1 | c.619C>T | p.Arg207Trp | missense_variant | Exon 3 of 14 | ENST00000616016.5 | NP_001372570.1 | |
SAMD11 | NM_001385640.1 | c.619C>T | p.Arg207Trp | missense_variant | Exon 3 of 14 | NP_001372569.1 | ||
SAMD11 | NM_152486.4 | c.82C>T | p.Arg28Trp | missense_variant | Exon 3 of 14 | NP_689699.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SAMD11 | ENST00000616016.5 | c.619C>T | p.Arg207Trp | missense_variant | Exon 3 of 14 | 5 | NM_001385641.1 | ENSP00000478421.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000125 AC: 2AN: 159672Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 85436
GnomAD4 exome AF: 0.0000114 AC: 16AN: 1404090Hom.: 0 Cov.: 31 AF XY: 0.0000115 AC XY: 8AN XY: 693198
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74476
ClinVar
Submissions by phenotype
not provided Uncertain:1
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. 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: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with SAMD11-related conditions. This variant is present in population databases (rs144245409, gnomAD 0.01%). This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 28 of the SAMD11 protein (p.Arg28Trp). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at