rs1046089
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004638.4(PRRC2A):c.5219G>A(p.Arg1740His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 1,613,872 control chromosomes in the GnomAD database, including 106,562 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). 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 -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRRC2A | NM_004638.4 | c.5219G>A | p.Arg1740His | missense_variant | 22/31 | ENST00000376033.3 | |
PRRC2A | NM_080686.3 | c.5219G>A | p.Arg1740His | missense_variant | 22/31 | ||
PRRC2A | XM_047419336.1 | c.5219G>A | p.Arg1740His | missense_variant | 22/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRRC2A | ENST00000376033.3 | c.5219G>A | p.Arg1740His | missense_variant | 22/31 | 1 | NM_004638.4 | P1 | |
PRRC2A | ENST00000376007.8 | c.5219G>A | p.Arg1740His | missense_variant | 22/31 | 1 | P1 | ||
PRRC2A | ENST00000484787.1 | n.630G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.399 AC: 60663AN: 151920Hom.: 12565 Cov.: 32
GnomAD3 exomes AF: 0.357 AC: 89663AN: 251378Hom.: 16895 AF XY: 0.346 AC XY: 47035AN XY: 135868
GnomAD4 exome AF: 0.354 AC: 517868AN: 1461834Hom.: 93991 Cov.: 68 AF XY: 0.349 AC XY: 253786AN XY: 727212
GnomAD4 genome ? AF: 0.399 AC: 60700AN: 152038Hom.: 12571 Cov.: 32 AF XY: 0.402 AC XY: 29892AN XY: 74310
ClinVar
Submissions by phenotype
PRRC2A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 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