chr6-31626021-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004638.4(PRRC2A):c.841C>T(p.Arg281Cys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,611,736 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. 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. R281H) has been classified as Uncertain significance.
Frequency
Consequence
NM_004638.4 missense, splice_region
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 | UniProt |
---|---|---|---|---|---|---|---|
PRRC2A | NM_004638.4 | c.841C>T | p.Arg281Cys | missense_variant, splice_region_variant | 9/31 | ENST00000376033.3 | |
PRRC2A | NM_080686.3 | c.841C>T | p.Arg281Cys | missense_variant, splice_region_variant | 9/31 | ||
PRRC2A | XM_047419336.1 | c.841C>T | p.Arg281Cys | missense_variant, splice_region_variant | 9/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRRC2A | ENST00000376033.3 | c.841C>T | p.Arg281Cys | missense_variant, splice_region_variant | 9/31 | 1 | NM_004638.4 | P1 | |
PRRC2A | ENST00000376007.8 | c.841C>T | p.Arg281Cys | missense_variant, splice_region_variant | 9/31 | 1 | P1 | ||
PRRC2A | ENST00000464890.1 | n.268C>T | non_coding_transcript_exon_variant | 1/3 | 2 | ||||
PRRC2A | ENST00000469577.5 | n.686C>T | splice_region_variant, non_coding_transcript_exon_variant | 7/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000490 AC: 12AN: 245034Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 133662
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1459486Hom.: 0 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 726112
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74436
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | The c.841C>T (p.R281C) alteration is located in exon 9 (coding exon 8) of the PRRC2A gene. This alteration results from a C to T substitution at nucleotide position 841, causing the arginine (R) at amino acid position 281 to be replaced by a cysteine (C). 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