22-44737015-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_181333.4(PRR5):c.935C>T(p.Ala312Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000687 in 1,600,340 control chromosomes in the GnomAD database, including 1 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 Uncertain significance (★).
Frequency
Consequence
NM_181333.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRR5 | NM_181333.4 | c.935C>T | p.Ala312Val | missense_variant | 8/8 | ENST00000336985.11 | |
PRR5-ARHGAP8 | NM_181334.6 | c.322+10381C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRR5 | ENST00000336985.11 | c.935C>T | p.Ala312Val | missense_variant | 8/8 | 1 | NM_181333.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000176 AC: 41AN: 233362Hom.: 0 AF XY: 0.000256 AC XY: 33AN XY: 128984
GnomAD4 exome AF: 0.0000725 AC: 105AN: 1448088Hom.: 1 Cov.: 32 AF XY: 0.000107 AC XY: 77AN XY: 718792
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152252Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 02, 2023 | The c.1004C>T (p.A335V) alteration is located in exon 10 (coding exon 9) of the PRR5 gene. This alteration results from a C to T substitution at nucleotide position 1004, causing the alanine (A) at amino acid position 335 to be replaced by a valine (V). 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