chr16-88715442-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001142864.4(PIEZO1):c.*163G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 935,476 control chromosomes in the GnomAD database, including 8,056 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.10 ( 910 hom., cov: 33)
Exomes 𝑓: 0.12 ( 7146 hom. )
Consequence
PIEZO1
NM_001142864.4 3_prime_UTR
NM_001142864.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.30
Genes affected
PIEZO1 (HGNC:28993): (piezo type mechanosensitive ion channel component 1 (Er blood group)) The protein encoded by this gene is a mechanically-activated ion channel that links mechanical forces to biological signals. The encoded protein contains 36 transmembrane domains and functions as a homotetramer. Defects in this gene have been associated with dehydrated hereditary stomatocytosis. [provided by RefSeq, Jul 2015]
CTU2 (HGNC:28005): (cytosolic thiouridylase subunit 2) This gene encodes a protein which is involved in the post-transcriptional modification of transfer RNAs (tRNAs). The encoded protein plays a role in thiolation of uridine residue present at the wobble position in a subset of tRNAs, resulting in enhanced codon reading accuracy. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
Variant 16-88715442-C-T is Benign according to our data. Variant chr16-88715442-C-T is described in ClinVar as [Benign]. Clinvar id is 1246797.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PIEZO1 | NM_001142864.4 | c.*163G>A | 3_prime_UTR_variant | 51/51 | ENST00000301015.14 | ||
CTU2 | NM_001012759.3 | downstream_gene_variant | ENST00000453996.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PIEZO1 | ENST00000301015.14 | c.*163G>A | 3_prime_UTR_variant | 51/51 | 1 | NM_001142864.4 | P1 | ||
CTU2 | ENST00000453996.7 | downstream_gene_variant | 1 | NM_001012759.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0999 AC: 15198AN: 152122Hom.: 908 Cov.: 33
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GnomAD4 exome AF: 0.125 AC: 97563AN: 783240Hom.: 7146 Cov.: 10 AF XY: 0.121 AC XY: 48084AN XY: 398194
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GnomAD4 genome AF: 0.0999 AC: 15208AN: 152236Hom.: 910 Cov.: 33 AF XY: 0.0966 AC XY: 7192AN XY: 74436
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at