rs371432372
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4BS1_Supporting
The NM_001378183.1(PIEZO2):c.152C>T(p.Thr51Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000545 in 1,531,728 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 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIEZO2 | NM_001378183.1 | c.152C>T | p.Thr51Met | missense_variant | Exon 2 of 56 | ENST00000674853.1 | NP_001365112.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIEZO2 | ENST00000674853.1 | c.152C>T | p.Thr51Met | missense_variant | Exon 2 of 56 | NM_001378183.1 | ENSP00000501957.1 |
Frequencies
GnomAD3 genomes AF: 0.000414 AC: 63AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000303 AC: 43AN: 141828Hom.: 0 AF XY: 0.000382 AC XY: 29AN XY: 75848
GnomAD4 exome AF: 0.000560 AC: 772AN: 1379592Hom.: 0 Cov.: 29 AF XY: 0.000556 AC XY: 379AN XY: 681126
GnomAD4 genome AF: 0.000414 AC: 63AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.000404 AC XY: 30AN XY: 74314
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
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Inborn genetic diseases Uncertain:1
The c.152C>T (p.T51M) alteration is located in exon 2 (coding exon 2) of the PIEZO2 gene. This alteration results from a C to T substitution at nucleotide position 152, causing the threonine (T) at amino acid position 51 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Arthrogryposis, distal, with impaired proprioception and touch Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at