16-88715618-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001142864.4(PIEZO1):c.7553G>A(p.Arg2518His) variant causes a missense change. The variant allele was found at a frequency of 0.000051 in 1,549,824 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2518P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001142864.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIEZO1 | ENST00000301015.14 | c.7553G>A | p.Arg2518His | missense_variant | Exon 51 of 51 | 1 | NM_001142864.4 | ENSP00000301015.9 | ||
CTU2 | ENST00000453996.7 | c.*367C>T | downstream_gene_variant | 1 | NM_001012759.3 | ENSP00000388320.2 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000523 AC: 8AN: 152992Hom.: 0 AF XY: 0.0000859 AC XY: 7AN XY: 81462
GnomAD4 exome AF: 0.0000501 AC: 70AN: 1397640Hom.: 0 Cov.: 32 AF XY: 0.0000522 AC XY: 36AN XY: 689316
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74344
ClinVar
Submissions by phenotype
Dehydrated hereditary stomatocytosis with or without pseudohyperkalemia and/or perinatal edema Uncertain:1
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at