rs11229
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004638.4(PRRC2A):āc.5568A>Cā(p.Gln1856His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,612,692 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. Q1856Q) has been classified as Benign.
Frequency
Consequence
NM_004638.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRRC2A | NM_004638.4 | c.5568A>C | p.Gln1856His | missense_variant | 25/31 | ENST00000376033.3 | |
PRRC2A | NM_080686.3 | c.5568A>C | p.Gln1856His | missense_variant | 25/31 | ||
PRRC2A | XM_047419336.1 | c.5568A>C | p.Gln1856His | missense_variant | 25/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRRC2A | ENST00000376033.3 | c.5568A>C | p.Gln1856His | missense_variant | 25/31 | 1 | NM_004638.4 | P1 | |
PRRC2A | ENST00000376007.8 | c.5568A>C | p.Gln1856His | missense_variant | 25/31 | 1 | P1 | ||
PRRC2A | ENST00000487089.1 | n.634A>C | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
PRRC2A | ENST00000487839.1 | n.502A>C | non_coding_transcript_exon_variant | 2/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151914Hom.: 0 Cov.: 31
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460778Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 726762
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151914Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74160
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at