Variant rs13280644 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_007332.3(TRPA1):c.2490G>A(p.Leu830=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0898 in 1,613,898 control chromosomes in the GnomAD database, including 7,458 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.068 ( 526 hom., cov: 32)

Exomes 𝑓: 0.092 ( 6932 hom. )

Consequence

TRPA1
NM_007332.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.444

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 8-72036353-C-T is Benign according to our data. Variant chr8-72036353-C-T is described in ClinVar as [Benign]. Clinvar id is 3056632.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.444 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPA1	NM_007332.3 linkuse as main transcript	c.2490G>A	p.Leu830=	synonymous_variant	21/27	ENST00000262209.5
MSC-AS1	NR_033652.1 linkuse as main transcript	n.1029-16186C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPA1	ENST00000262209.5 linkuse as main transcript	c.2490G>A	p.Leu830=	synonymous_variant	21/27	1	NM_007332.3	P1
MSC-AS1	ENST00000518916.5 linkuse as main transcript	n.392-16186C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0685

AC:

10431

AN:

152168

Hom.:

527

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0174

Gnomad AMI

AF:

0.0507

Gnomad AMR

AF:

0.0863

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.0471

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.0989

Gnomad OTH

AF:

0.0876

GnomAD3 exomes

AF:

0.0773

AC:

19404

AN:

251124

Hom.:

956

AF XY:

0.0826

AC XY:

11215

AN XY:

135738

show subpopulations

Gnomad AFR exome

AF:

0.0148

Gnomad AMR exome

AF:

0.0598

Gnomad ASJ exome

AF:

0.113

Gnomad EAS exome

AF:

0.000435

Gnomad SAS exome

AF:

0.113

Gnomad FIN exome

AF:

0.0441

Gnomad NFE exome

AF:

0.0964

Gnomad OTH exome

AF:

0.0944

GnomAD4 exome

AF:

0.0920

AC:

134503

AN:

1461612

Hom.:

6932

Cov.:

AF XY:

0.0935

AC XY:

67993

AN XY:

727112

show subpopulations

Gnomad4 AFR exome

AF:

0.0168

Gnomad4 AMR exome

AF:

0.0624

Gnomad4 ASJ exome

AF:

0.112

Gnomad4 EAS exome

AF:

0.000327

Gnomad4 SAS exome

AF:

0.112

Gnomad4 FIN exome

AF:

0.0454

Gnomad4 NFE exome

AF:

0.0990

Gnomad4 OTH exome

AF:

0.0879

GnomAD4 genome

AF:

0.0685

AC:

10430

AN:

152286

Hom.:

526

Cov.:

AF XY:

0.0673

AC XY:

5008

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.0174

Gnomad4 AMR

AF:

0.0862

Gnomad4 ASJ

AF:

0.114

Gnomad4 EAS

AF:

0.00154

Gnomad4 SAS

AF:

0.103

Gnomad4 FIN

AF:

0.0471

Gnomad4 NFE

AF:

0.0989

Gnomad4 OTH

AF:

0.0866

Alfa

AF:

0.0964

Hom.:

1270

Bravo

AF:

0.0663

Asia WGS

AF:

0.0510

AC:

176

AN:

3478

EpiCase

AF:

0.102

EpiControl

AF:

0.105

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

TRPA1-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 28, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

6.3

DANN

Benign

0.84

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