Variant 8-72026097-G-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 ENST00000262209.5(TRPA1):c.2938-24C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 1,575,902 control chromosomes in the GnomAD database, including 54,975 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 4181 hom., cov: 32)

Exomes 𝑓: 0.26 ( 50794 hom. )

Consequence

TRPA1
ENST00000262209.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 2.01

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=-0.84).

BP6

Variant 8-72026097-G-C is Benign according to our data. Variant chr8-72026097-G-C is described in ClinVar as [Benign]. Clinvar id is 1342277.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.333 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.2938-24C>G		intron_variant		ENST00000262209.5	NP_015628.2
MSC-AS1	NR_033652.1 linkuse as main transcript	n.1029-26442G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRPA1	ENST00000262209.5 linkuse as main transcript	c.2938-24C>G		intron_variant		1	NM_007332.3	ENSP00000262209	P1
MSC-AS1	ENST00000518916.5 linkuse as main transcript	n.392-26442G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

34143

AN:

152108

Hom.:

4180

Cov.:

show subpopulations

Gnomad AFR

AF:

0.145

Gnomad AMI

AF:

0.158

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.368

Gnomad EAS

AF:

0.346

Gnomad SAS

AF:

0.310

Gnomad FIN

AF:

0.200

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.263

Gnomad OTH

AF:

0.254

GnomAD3 exomes

AF:

0.252

AC:

62748

AN:

249216

Hom.:

8533

AF XY:

0.262

AC XY:

35327

AN XY:

134640

show subpopulations

Gnomad AFR exome

AF:

0.142

Gnomad AMR exome

AF:

0.138

Gnomad ASJ exome

AF:

0.376

Gnomad EAS exome

AF:

0.358

Gnomad SAS exome

AF:

0.315

Gnomad FIN exome

AF:

0.216

Gnomad NFE exome

AF:

0.263

Gnomad OTH exome

AF:

0.254

GnomAD4 exome

AF:

0.262

AC:

373350

AN:

1423676

Hom.:

50794

Cov.:

AF XY:

0.266

AC XY:

188966

AN XY:

710592

show subpopulations

Gnomad4 AFR exome

AF:

0.141

Gnomad4 AMR exome

AF:

0.143

Gnomad4 ASJ exome

AF:

0.377

Gnomad4 EAS exome

AF:

0.365

Gnomad4 SAS exome

AF:

0.321

Gnomad4 FIN exome

AF:

0.218

Gnomad4 NFE exome

AF:

0.261

Gnomad4 OTH exome

AF:

0.266

GnomAD4 genome

AF:

0.224

AC:

34165

AN:

152226

Hom.:

4181

Cov.:

AF XY:

0.225

AC XY:

16753

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.145

Gnomad4 AMR

AF:

0.178

Gnomad4 ASJ

AF:

0.368

Gnomad4 EAS

AF:

0.346

Gnomad4 SAS

AF:

0.309

Gnomad4 FIN

AF:

0.200

Gnomad4 NFE

AF:

0.263

Gnomad4 OTH

AF:

0.255

Alfa

AF:

0.202

Hom.:

704

Bravo

AF:

0.217

Asia WGS

AF:

0.266

AC:

924

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

-0.84

CADD

Benign

7.1

DANN

Benign

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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