Variant chr8-72026122-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_007332.3(TRPA1):c.2938-49T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 1,411,966 control chromosomes in the GnomAD database, including 43,613 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.23 ( 4269 hom., cov: 32)

Exomes 𝑓: 0.25 ( 39344 hom. )

Consequence

TRPA1
NM_007332.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.02

Variant links:

Genes affected

TRPA1 (HGNC:497): (transient receptor potential cation channel subfamily A member 1) The structure of the protein encoded by this gene is highly related to both the protein ankyrin and transmembrane proteins. The specific function of this protein has not yet been determined; however, studies indicate the function may involve a role in signal transduction and growth control. [provided by RefSeq, Jul 2008]

TRPA1 links:

MSC-AS1 (HGNC:):

MSC-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 8-72026122-A-C is Benign according to our data. Variant chr8-72026122-A-C is described in ClinVar as [Benign]. Clinvar id is 1342278.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRPA1	NM_007332.3 linkuse as main transcript	c.2938-49T>G		intron_variant		ENST00000262209.5	NP_015628.2	O75762

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRPA1	ENST00000262209.5 linkuse as main transcript	c.2938-49T>G		intron_variant		1	NM_007332.3	ENSP00000262209.4		O75762

Frequencies

GnomAD3 genomes

AF:

0.228

AC:

34735

AN:

152018

Hom.:

4263

Cov.:

show subpopulations

Gnomad AFR

AF:

0.152

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.256

Gnomad ASJ

AF:

0.234

Gnomad EAS

AF:

0.344

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.335

Gnomad MID

AF:

0.153

Gnomad NFE

AF:

0.250

Gnomad OTH

AF:

0.207

GnomAD3 exomes

AF:

0.250

AC:

60388

AN:

241868

Hom.:

8022

AF XY:

0.243

AC XY:

31820

AN XY:

130810

show subpopulations

Gnomad AFR exome

AF:

0.149

Gnomad AMR exome

AF:

0.291

Gnomad ASJ exome

AF:

0.230

Gnomad EAS exome

AF:

0.342

Gnomad SAS exome

AF:

0.137

Gnomad FIN exome

AF:

0.326

Gnomad NFE exome

AF:

0.255

Gnomad OTH exome

AF:

0.240

GnomAD4 exome

AF:

0.246

AC:

309553

AN:

1259830

Hom.:

39344

Cov.:

AF XY:

0.242

AC XY:

153891

AN XY:

636906

show subpopulations

Gnomad4 AFR exome

AF:

0.154

Gnomad4 AMR exome

AF:

0.284

Gnomad4 ASJ exome

AF:

0.230

Gnomad4 EAS exome

AF:

0.358

Gnomad4 SAS exome

AF:

0.139

Gnomad4 FIN exome

AF:

0.327

Gnomad4 NFE exome

AF:

0.249

Gnomad4 OTH exome

AF:

0.234

GnomAD4 genome

AF:

0.229

AC:

34771

AN:

152136

Hom.:

4269

Cov.:

AF XY:

0.232

AC XY:

17256

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.152

Gnomad4 AMR

AF:

0.257

Gnomad4 ASJ

AF:

0.234

Gnomad4 EAS

AF:

0.345

Gnomad4 SAS

AF:

0.137

Gnomad4 FIN

AF:

0.335

Gnomad4 NFE

AF:

0.250

Gnomad4 OTH

AF:

0.207

Alfa

AF:

0.244

Hom.:

857

Bravo

AF:

0.223

Asia WGS

AF:

0.247

AC:

861

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Familial episodic pain syndrome with predominantly upper body involvement

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.0

DANN

Benign

0.71

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over