18-10791216-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_001378183.1(PIEZO2):c.1867G>A(p.Glu623Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000723 in 1,383,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001378183.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIEZO2 | NM_001378183.1 | c.1867G>A | p.Glu623Lys | missense_variant | 14/56 | ENST00000674853.1 | NP_001365112.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIEZO2 | ENST00000674853.1 | c.1867G>A | p.Glu623Lys | missense_variant | 14/56 | NM_001378183.1 | ENSP00000501957.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 7.23e-7 AC: 1AN: 1383066Hom.: 0 Cov.: 30 AF XY: 0.00000147 AC XY: 1AN XY: 682424
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Arthrogryposis, distal, with impaired proprioception and touch Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Dec 15, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at