6-31625522-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004638.4(PRRC2A):āc.670A>Cā(p.Lys224Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000007 in 1,428,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004638.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRRC2A | NM_004638.4 | c.670A>C | p.Lys224Gln | missense_variant | 7/31 | ENST00000376033.3 | NP_004629.3 | |
PRRC2A | NM_080686.3 | c.670A>C | p.Lys224Gln | missense_variant | 7/31 | NP_542417.2 | ||
PRRC2A | XM_047419336.1 | c.670A>C | p.Lys224Gln | missense_variant | 7/30 | XP_047275292.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRRC2A | ENST00000376033.3 | c.670A>C | p.Lys224Gln | missense_variant | 7/31 | 1 | NM_004638.4 | ENSP00000365201.2 | ||
ENSG00000289282 | ENST00000687518.1 | c.*23A>C | downstream_gene_variant | ENSP00000509222.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000434 AC: 1AN: 230622Hom.: 0 AF XY: 0.00000810 AC XY: 1AN XY: 123506
GnomAD4 exome AF: 7.00e-7 AC: 1AN: 1428984Hom.: 0 Cov.: 33 AF XY: 0.00000142 AC XY: 1AN XY: 706154
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2022 | The c.670A>C (p.K224Q) alteration is located in exon 7 (coding exon 6) of the PRRC2A gene. This alteration results from a A to C substitution at nucleotide position 670, causing the lysine (K) at amino acid position 224 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at