chr22-44737105-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_181333.4(PRR5):c.1025G>A(p.Arg342His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000605 in 1,612,104 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (★).
Frequency
Consequence
NM_181333.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRR5 | NM_181333.4 | c.1025G>A | p.Arg342His | missense_variant | 8/8 | ENST00000336985.11 | |
PRR5-ARHGAP8 | NM_181334.6 | c.322+10471G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRR5 | ENST00000336985.11 | c.1025G>A | p.Arg342His | missense_variant | 8/8 | 1 | NM_181333.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000453 AC: 69AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000414 AC: 101AN: 243856Hom.: 0 AF XY: 0.000466 AC XY: 62AN XY: 133156
GnomAD4 exome AF: 0.000621 AC: 906AN: 1459782Hom.: 0 Cov.: 32 AF XY: 0.000594 AC XY: 431AN XY: 726192
GnomAD4 genome ? AF: 0.000453 AC: 69AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.000309 AC XY: 23AN XY: 74484
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at