22-44737039-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_181333.4(PRR5):c.959G>C(p.Ser320Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000312 in 1,604,004 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 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.959G>C | p.Ser320Thr | missense_variant | 8/8 | ENST00000336985.11 | |
PRR5-ARHGAP8 | NM_181334.6 | c.322+10405G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRR5 | ENST00000336985.11 | c.959G>C | p.Ser320Thr | missense_variant | 8/8 | 1 | NM_181333.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000377 AC: 9AN: 238582Hom.: 0 AF XY: 0.0000305 AC XY: 4AN XY: 131254
GnomAD4 exome AF: 0.00000276 AC: 4AN: 1451788Hom.: 0 Cov.: 32 AF XY: 0.00000416 AC XY: 3AN XY: 721102
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2023 | The c.1028G>C (p.S343T) alteration is located in exon 10 (coding exon 9) of the PRR5 gene. This alteration results from a G to C substitution at nucleotide position 1028, causing the serine (S) at amino acid position 343 to be replaced by a threonine (T). 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