Variant chr8-72029975-G-T 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.2869-6C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 1,610,630 control chromosomes in the GnomAD database, including 299,729 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.63 ( 30320 hom., cov: 32)

Exomes 𝑓: 0.61 ( 269409 hom. )

Consequence

TRPA1
NM_007332.3 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.001980

Clinical Significance

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

Conservation

PhyloP100: -0.483

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 8-72029975-G-T is Benign according to our data. Variant chr8-72029975-G-T is described in ClinVar as [Benign]. Clinvar id is 1342279.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.73 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.2869-6C>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000262209.5	NP_015628.2
MSC-AS1	NR_033652.1 linkuse as main transcript	n.1029-22564G>T		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.2869-6C>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_007332.3	ENSP00000262209	P1
MSC-AS1	ENST00000518916.5 linkuse as main transcript	n.392-22564G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.628

AC:

95450

AN:

151900

Hom.:

30277

Cov.:

show subpopulations

Gnomad AFR

AF:

0.656

Gnomad AMI

AF:

0.533

Gnomad AMR

AF:

0.741

Gnomad ASJ

AF:

0.649

Gnomad EAS

AF:

0.692

Gnomad SAS

AF:

0.672

Gnomad FIN

AF:

0.552

Gnomad MID

AF:

0.682

Gnomad NFE

AF:

0.590

Gnomad OTH

AF:

0.638

GnomAD3 exomes

AF:

0.643

AC:

161375

AN:

250870

Hom.:

52791

AF XY:

0.637

AC XY:

86312

AN XY:

135576

show subpopulations

Gnomad AFR exome

AF:

0.651

Gnomad AMR exome

AF:

0.806

Gnomad ASJ exome

AF:

0.657

Gnomad EAS exome

AF:

0.686

Gnomad SAS exome

AF:

0.669

Gnomad FIN exome

AF:

0.559

Gnomad NFE exome

AF:

0.594

Gnomad OTH exome

AF:

0.634

GnomAD4 exome

AF:

0.605

AC:

882891

AN:

1458610

Hom.:

269409

Cov.:

AF XY:

0.606

AC XY:

439736

AN XY:

725742

show subpopulations

Gnomad4 AFR exome

AF:

0.659

Gnomad4 AMR exome

AF:

0.798

Gnomad4 ASJ exome

AF:

0.656

Gnomad4 EAS exome

AF:

0.671

Gnomad4 SAS exome

AF:

0.667

Gnomad4 FIN exome

AF:

0.567

Gnomad4 NFE exome

AF:

0.588

Gnomad4 OTH exome

AF:

0.620

GnomAD4 genome

AF:

0.628

AC:

95541

AN:

152020

Hom.:

30320

Cov.:

AF XY:

0.631

AC XY:

46870

AN XY:

74298

show subpopulations

Gnomad4 AFR

AF:

0.656

Gnomad4 AMR

AF:

0.741

Gnomad4 ASJ

AF:

0.649

Gnomad4 EAS

AF:

0.693

Gnomad4 SAS

AF:

0.672

Gnomad4 FIN

AF:

0.552

Gnomad4 NFE

AF:

0.590

Gnomad4 OTH

AF:

0.636

Alfa

AF:

0.583

Hom.:

7131

Bravo

AF:

0.643

Asia WGS

AF:

0.696

AC:

2422

AN:

3476

EpiCase

AF:

0.588

EpiControl

AF:

0.587

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

-0.80

CADD

Benign

0.23

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.0020

dbscSNV1_RF

Benign

0.26

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