chr6-31625544-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004638.4(PRRC2A):c.692C>T(p.Pro231Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000698 in 1,575,178 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P231S) has been classified as Uncertain significance.
Frequency
Consequence
NM_004638.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRRC2A | NM_004638.4 | c.692C>T | p.Pro231Leu | missense_variant | 7/31 | ENST00000376033.3 | |
PRRC2A | NM_080686.3 | c.692C>T | p.Pro231Leu | missense_variant | 7/31 | ||
PRRC2A | XM_047419336.1 | c.692C>T | p.Pro231Leu | missense_variant | 7/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRRC2A | ENST00000376033.3 | c.692C>T | p.Pro231Leu | missense_variant | 7/31 | 1 | NM_004638.4 | P1 | |
ENST00000687518.1 | downstream_gene_variant | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000179 AC: 4AN: 223928Hom.: 0 AF XY: 0.0000250 AC XY: 3AN XY: 119864
GnomAD4 exome AF: 0.00000632 AC: 9AN: 1423024Hom.: 0 Cov.: 33 AF XY: 0.00000712 AC XY: 5AN XY: 702680
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2023 | The c.692C>T (p.P231L) alteration is located in exon 7 (coding exon 6) of the PRRC2A gene. This alteration results from a C to T substitution at nucleotide position 692, causing the proline (P) at amino acid position 231 to be replaced by a leucine (L). 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