rs2736158
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004638.4(PRRC2A):āc.3854G>Cā(p.Gly1285Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.04 in 1,609,644 control chromosomes in the GnomAD database, including 2,178 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004638.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRRC2A | NM_004638.4 | c.3854G>C | p.Gly1285Ala | missense_variant | 16/31 | ENST00000376033.3 | |
PRRC2A | NM_080686.3 | c.3854G>C | p.Gly1285Ala | missense_variant | 16/31 | ||
PRRC2A | XM_047419336.1 | c.3854G>C | p.Gly1285Ala | missense_variant | 16/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRRC2A | ENST00000376033.3 | c.3854G>C | p.Gly1285Ala | missense_variant | 16/31 | 1 | NM_004638.4 | P1 | |
PRRC2A | ENST00000376007.8 | c.3854G>C | p.Gly1285Ala | missense_variant | 16/31 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0662 AC: 10070AN: 152066Hom.: 509 Cov.: 32
GnomAD3 exomes AF: 0.0489 AC: 11941AN: 244426Hom.: 583 AF XY: 0.0473 AC XY: 6305AN XY: 133188
GnomAD4 exome AF: 0.0373 AC: 54378AN: 1457460Hom.: 1669 Cov.: 33 AF XY: 0.0374 AC XY: 27084AN XY: 724604
GnomAD4 genome AF: 0.0662 AC: 10074AN: 152184Hom.: 509 Cov.: 32 AF XY: 0.0663 AC XY: 4928AN XY: 74384
ClinVar
Submissions by phenotype
PRRC2A-related disorder Benign:1
Benign, criteria provided, single submitter | 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 18, 2020 | This variant is associated with the following publications: (PMID: 23221128) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at