chr11-36462518-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001160167.2(PRR5L):c.889T>G(p.Ser297Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000329 in 1,608,822 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S297S) has been classified as Benign.
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.889T>G | p.Ser297Ala | missense_variant | 9/9 | ENST00000530639.6 | |
PRR5L | NM_024841.5 | c.889T>G | p.Ser297Ala | missense_variant | 10/10 | ||
PRR5L | NM_001160168.2 | c.505T>G | p.Ser169Ala | missense_variant | 6/6 | ||
PRR5L | NM_001160169.1 | c.*144T>G | 3_prime_UTR_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRR5L | ENST00000530639.6 | c.889T>G | p.Ser297Ala | missense_variant | 9/9 | 2 | NM_001160167.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000173 AC: 42AN: 243092Hom.: 0 AF XY: 0.000144 AC XY: 19AN XY: 131682
GnomAD4 exome AF: 0.0000330 AC: 48AN: 1456532Hom.: 0 Cov.: 30 AF XY: 0.0000318 AC XY: 23AN XY: 724166
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2023 | The c.889T>G (p.S297A) alteration is located in exon 9 (coding exon 8) of the PRR5L gene. This alteration results from a T to G substitution at nucleotide position 889, causing the serine (S) at amino acid position 297 to be replaced by an alanine (A). 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