chr12-10847181-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_007244.3(PRR4):c.287G>A(p.Arg96Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 1,612,768 control chromosomes in the GnomAD database, including 268,556 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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_007244.3 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 |
---|---|---|---|---|---|---|---|
PRR4 | NM_007244.3 | c.287G>A | p.Arg96Gln | missense_variant | 3/4 | ENST00000228811.8 | |
PRH1-PRR4 | NR_037918.2 | n.1407G>A | non_coding_transcript_exon_variant | 9/10 | |||
PRR4 | NM_001098538.3 | c.101-46G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRR4 | ENST00000228811.8 | c.287G>A | p.Arg96Gln | missense_variant | 3/4 | 1 | NM_007244.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.490 AC: 74200AN: 151578Hom.: 20673 Cov.: 29
GnomAD3 exomes AF: 0.597 AC: 148759AN: 249200Hom.: 46033 AF XY: 0.605 AC XY: 81740AN XY: 135182
GnomAD4 exome AF: 0.578 AC: 844212AN: 1461072Hom.: 247888 Cov.: 69 AF XY: 0.582 AC XY: 422903AN XY: 726814
GnomAD4 genome ? AF: 0.489 AC: 74201AN: 151696Hom.: 20668 Cov.: 29 AF XY: 0.498 AC XY: 36861AN XY: 74092
ClinVar
Submissions by phenotype
PRR4-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 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