Variant rs3735943 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000262209.5(TRPA1):c.1630C>T(p.Leu544=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 1,609,828 control chromosomes in the GnomAD database, including 212,152 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.52 ( 20935 hom., cov: 32)

Exomes 𝑓: 0.51 ( 191217 hom. )

Consequence

TRPA1
ENST00000262209.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.73

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 8-72053767-G-A is Benign according to our data. Variant chr8-72053767-G-A is described in ClinVar as [Benign]. Clinvar id is 1342282.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.73 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 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.1630C>T	p.Leu544=	synonymous_variant	13/27	ENST00000262209.5	NP_015628.2
MSC-AS1	NR_033652.1 linkuse as main transcript	n.2257G>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.1630C>T	p.Leu544=	synonymous_variant	13/27	1	NM_007332.3	ENSP00000262209	P1
MSC-AS1	ENST00000518916.5 linkuse as main transcript	n.469+1151G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.519

AC:

78883

AN:

151914

Hom.:

20901

Cov.:

show subpopulations

Gnomad AFR

AF:

0.499

Gnomad AMI

AF:

0.496

Gnomad AMR

AF:

0.637

Gnomad ASJ

AF:

0.532

Gnomad EAS

AF:

0.691

Gnomad SAS

AF:

0.571

Gnomad FIN

AF:

0.504

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.490

Gnomad OTH

AF:

0.522

GnomAD3 exomes

AF:

0.554

AC:

138305

AN:

249818

Hom.:

39427

AF XY:

0.545

AC XY:

73531

AN XY:

134960

show subpopulations

Gnomad AFR exome

AF:

0.493

Gnomad AMR exome

AF:

0.736

Gnomad ASJ exome

AF:

0.539

Gnomad EAS exome

AF:

0.684

Gnomad SAS exome

AF:

0.556

Gnomad FIN exome

AF:

0.514

Gnomad NFE exome

AF:

0.495

Gnomad OTH exome

AF:

0.531

GnomAD4 exome

AF:

0.509

AC:

741460

AN:

1457796

Hom.:

191217

Cov.:

AF XY:

0.508

AC XY:

368715

AN XY:

725228

show subpopulations

Gnomad4 AFR exome

AF:

0.497

Gnomad4 AMR exome

AF:

0.725

Gnomad4 ASJ exome

AF:

0.540

Gnomad4 EAS exome

AF:

0.671

Gnomad4 SAS exome

AF:

0.555

Gnomad4 FIN exome

AF:

0.520

Gnomad4 NFE exome

AF:

0.489

Gnomad4 OTH exome

AF:

0.522

GnomAD4 genome

AF:

0.519

AC:

78966

AN:

152032

Hom.:

20935

Cov.:

AF XY:

0.524

AC XY:

38936

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.500

Gnomad4 AMR

AF:

0.637

Gnomad4 ASJ

AF:

0.532

Gnomad4 EAS

AF:

0.692

Gnomad4 SAS

AF:

0.570

Gnomad4 FIN

AF:

0.504

Gnomad4 NFE

AF:

0.490

Gnomad4 OTH

AF:

0.521

Alfa

AF:

0.504

Hom.:

32400

Bravo

AF:

0.531

Asia WGS

AF:

0.640

AC:

2227

AN:

3478

EpiCase

AF:

0.486

EpiControl

AF:

0.479

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

-0.79

CADD

Benign

7.1

DANN

Benign

0.79

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