rs10954696
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_033026.6(PCLO):c.7423G>A(p.Val2475Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 1,611,864 control chromosomes in the GnomAD database, including 107,744 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_033026.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCLO | NM_033026.6 | c.7423G>A | p.Val2475Ile | missense_variant | 5/25 | ENST00000333891.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCLO | ENST00000333891.14 | c.7423G>A | p.Val2475Ile | missense_variant | 5/25 | 2 | NM_033026.6 | P1 | |
PCLO | ENST00000423517.6 | c.7423G>A | p.Val2475Ile | missense_variant | 5/20 | 5 |
Frequencies
GnomAD3 genomes AF: 0.307 AC: 46351AN: 151158Hom.: 8173 Cov.: 29
GnomAD3 exomes AF: 0.369 AC: 91943AN: 248846Hom.: 17701 AF XY: 0.372 AC XY: 50219AN XY: 134986
GnomAD4 exome AF: 0.366 AC: 534561AN: 1460588Hom.: 99562 Cov.: 41 AF XY: 0.367 AC XY: 266747AN XY: 726650
GnomAD4 genome AF: 0.307 AC: 46372AN: 151276Hom.: 8182 Cov.: 29 AF XY: 0.312 AC XY: 23074AN XY: 73854
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 02, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at