Variant rs3735942 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 ENST00000262209.5(TRPA1):c.1644+15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 1,586,502 control chromosomes in the GnomAD database, including 102,778 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.37 ( 10927 hom., cov: 32)

Exomes 𝑓: 0.35 ( 91851 hom. )

Consequence

TRPA1
ENST00000262209.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.554

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:48724): (MSC antisense RNA 1)

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=-0.86).

BP6

Variant 8-72053738-G-A is Benign according to our data. Variant chr8-72053738-G-A is described in ClinVar as [Benign]. Clinvar id is 1342281.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 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.1644+15C>T		intron_variant		ENST00000262209.5	NP_015628.2
MSC-AS1	NR_033652.1 linkuse as main transcript	n.2228G>A		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRPA1	ENST00000262209.5 linkuse as main transcript	c.1644+15C>T		intron_variant		1	NM_007332.3	ENSP00000262209	P1
MSC-AS1	ENST00000518916.5 linkuse as main transcript	n.469+1122G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.370

AC:

56278

AN:

151962

Hom.:

10903

Cov.:

show subpopulations

Gnomad AFR

AF:

0.366

Gnomad AMI

AF:

0.421

Gnomad AMR

AF:

0.505

Gnomad ASJ

AF:

0.273

Gnomad EAS

AF:

0.547

Gnomad SAS

AF:

0.356

Gnomad FIN

AF:

0.414

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.329

Gnomad OTH

AF:

0.351

GnomAD3 exomes

AF:

0.398

AC:

98558

AN:

247362

Hom.:

21490

AF XY:

0.383

AC XY:

51157

AN XY:

133520

show subpopulations

Gnomad AFR exome

AF:

0.360

Gnomad AMR exome

AF:

0.638

Gnomad ASJ exome

AF:

0.272

Gnomad EAS exome

AF:

0.553

Gnomad SAS exome

AF:

0.342

Gnomad FIN exome

AF:

0.411

Gnomad NFE exome

AF:

0.332

Gnomad OTH exome

AF:

0.363

GnomAD4 exome

AF:

0.350

AC:

502436

AN:

1434422

Hom.:

91851

Cov.:

AF XY:

0.347

AC XY:

248008

AN XY:

714740

show subpopulations

Gnomad4 AFR exome

AF:

0.366

Gnomad4 AMR exome

AF:

0.622

Gnomad4 ASJ exome

AF:

0.273

Gnomad4 EAS exome

AF:

0.546

Gnomad4 SAS exome

AF:

0.342

Gnomad4 FIN exome

AF:

0.415

Gnomad4 NFE exome

AF:

0.331

Gnomad4 OTH exome

AF:

0.351

GnomAD4 genome

AF:

0.370

AC:

56344

AN:

152080

Hom.:

10927

Cov.:

AF XY:

0.376

AC XY:

27963

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.366

Gnomad4 AMR

AF:

0.505

Gnomad4 ASJ

AF:

0.273

Gnomad4 EAS

AF:

0.548

Gnomad4 SAS

AF:

0.355

Gnomad4 FIN

AF:

0.414

Gnomad4 NFE

AF:

0.329

Gnomad4 OTH

AF:

0.348

Alfa

AF:

0.333

Hom.:

15736

Bravo

AF:

0.382

Asia WGS

AF:

0.465

AC:

1616

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

-0.86

CADD

Benign

3.4

DANN

Benign

0.72

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