chr6-31625488-G-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The ENST00000687518.1(ENSG00000289282):c.382G>T(p.Ala128Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0386 in 1,588,870 control chromosomes in the GnomAD database, including 1,355 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/6 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A128V) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000687518.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRRC2A | NM_004638.4 | c.636G>T | p.Gly212Gly | synonymous_variant | Exon 7 of 31 | ENST00000376033.3 | NP_004629.3 | |
PRRC2A | NM_080686.3 | c.636G>T | p.Gly212Gly | synonymous_variant | Exon 7 of 31 | NP_542417.2 | ||
PRRC2A | XM_047419336.1 | c.636G>T | p.Gly212Gly | synonymous_variant | Exon 7 of 30 | XP_047275292.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENSG00000289282 | ENST00000687518.1 | c.382G>T | p.Ala128Ser | missense_variant | Exon 5 of 5 | ENSP00000509222.1 | ||||
PRRC2A | ENST00000376033.3 | c.636G>T | p.Gly212Gly | synonymous_variant | Exon 7 of 31 | 1 | NM_004638.4 | ENSP00000365201.2 |
Frequencies
GnomAD3 genomes AF: 0.0302 AC: 4589AN: 152168Hom.: 99 Cov.: 32
GnomAD3 exomes AF: 0.0319 AC: 7545AN: 236408Hom.: 171 AF XY: 0.0332 AC XY: 4205AN XY: 126714
GnomAD4 exome AF: 0.0395 AC: 56800AN: 1436584Hom.: 1256 Cov.: 33 AF XY: 0.0392 AC XY: 27850AN XY: 710642
GnomAD4 genome AF: 0.0301 AC: 4589AN: 152286Hom.: 99 Cov.: 32 AF XY: 0.0288 AC XY: 2142AN XY: 74478
ClinVar
Submissions by phenotype
PRRC2A-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 27, 2019 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at