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GeneBe

chr18-10746919-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001378183.1(PIEZO2):​c.4424+1552G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 151,726 control chromosomes in the GnomAD database, including 32,399 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.63 ( 32399 hom., cov: 32)

Consequence

PIEZO2
NM_001378183.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.533
Variant links:
Genes affected
PIEZO2 (HGNC:26270): (piezo type mechanosensitive ion channel component 2) The protein encoded by this gene contains more than thirty transmembrane domains and likely functions as part of mechanically-activated (MA) cation channels. These channels serve to connect mechanical forces to biological signals. The encoded protein quickly adapts MA currents in somatosensory neurons. Defects in this gene are a cause of type 5 distal arthrogryposis. Several alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Feb 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PIEZO2NM_001378183.1 linkuse as main transcriptc.4424+1552G>A intron_variant ENST00000674853.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PIEZO2ENST00000674853.1 linkuse as main transcriptc.4424+1552G>A intron_variant NM_001378183.1

Frequencies

GnomAD3 genomes
AF:
0.632
AC:
95813
AN:
151608
Hom.:
32350
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.887
Gnomad AMI
AF:
0.596
Gnomad AMR
AF:
0.489
Gnomad ASJ
AF:
0.561
Gnomad EAS
AF:
0.695
Gnomad SAS
AF:
0.475
Gnomad FIN
AF:
0.485
Gnomad MID
AF:
0.661
Gnomad NFE
AF:
0.543
Gnomad OTH
AF:
0.600
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.632
AC:
95908
AN:
151726
Hom.:
32399
Cov.:
32
AF XY:
0.626
AC XY:
46406
AN XY:
74118
show subpopulations
Gnomad4 AFR
AF:
0.887
Gnomad4 AMR
AF:
0.488
Gnomad4 ASJ
AF:
0.561
Gnomad4 EAS
AF:
0.695
Gnomad4 SAS
AF:
0.476
Gnomad4 FIN
AF:
0.485
Gnomad4 NFE
AF:
0.543
Gnomad4 OTH
AF:
0.606
Alfa
AF:
0.558
Hom.:
11860
Bravo
AF:
0.647
Asia WGS
AF:
0.654
AC:
2276
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.94
DANN
Benign
0.46

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs8086878; hg19: chr18-10746917; API