chr11-36462576-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001160167.2(PRR5L):c.947C>A(p.Ala316Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000602 in 1,612,876 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001160167.2 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 |
---|---|---|---|---|---|---|---|
PRR5L | NM_001160167.2 | c.947C>A | p.Ala316Asp | missense_variant | 9/9 | ENST00000530639.6 | |
PRR5L | NM_024841.5 | c.947C>A | p.Ala316Asp | missense_variant | 10/10 | ||
PRR5L | NM_001160168.2 | c.563C>A | p.Ala188Asp | missense_variant | 6/6 | ||
PRR5L | NM_001160169.1 | c.*202C>A | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRR5L | ENST00000530639.6 | c.947C>A | p.Ala316Asp | missense_variant | 9/9 | 2 | NM_001160167.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000329 AC: 50AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000327 AC: 81AN: 247566Hom.: 0 AF XY: 0.000313 AC XY: 42AN XY: 134276
GnomAD4 exome AF: 0.000631 AC: 921AN: 1460694Hom.: 0 Cov.: 30 AF XY: 0.000572 AC XY: 416AN XY: 726650
GnomAD4 genome AF: 0.000329 AC: 50AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.000323 AC XY: 24AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.947C>A (p.A316D) alteration is located in exon 9 (coding exon 8) of the PRR5L gene. This alteration results from a C to A substitution at nucleotide position 947, causing the alanine (A) at amino acid position 316 to be replaced by an aspartic acid (D). 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