rs1373302

Variant names:

• chr8-72045481-T-A
• rs1373302
• NM_007332.3:c.2061+1032A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007332.3(TRPA1):​c.2061+1032A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 150,458 control chromosomes in the GnomAD database, including 10,995 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.37 (10995 hom., cov: 27)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94
• Publications: 8 publications found

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]

MSC-AS1 (HGNC:48724): (MSC antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPA1	NM_007332.3	c.2061+1032A>T		intron_variant	Intron 17 of 26	ENST00000262209.5	NP_015628.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPA1	ENST00000262209.5	c.2061+1032A>T		intron_variant	Intron 17 of 26	1	NM_007332.3	ENSP00000262209.4

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56174 AN: 150340 Hom.: 10982 Cov.: 27

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.354

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.374 AC: 56222 AN: 150458 Hom.: 10995 Cov.: 27 AF XY: 0.379 AC XY: 27822 AN XY: 73376

African (AFR) AF: 0.379 AC: 15518 AN: 40958

American (AMR) AF: 0.506 AC: 7576 AN: 14962

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 927 AN: 3448

East Asian (EAS) AF: 0.547 AC: 2796 AN: 5114

South Asian (SAS) AF: 0.354 AC: 1671 AN: 4722

European-Finnish (FIN) AF: 0.413 AC: 4283 AN: 10380

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22259 AN: 67590

Other (OTH) AF: 0.352 AC: 733 AN: 2082

Alfa AF: 0.364 Hom.: 1272

Bravo AF: 0.386

Asia WGS AF: 0.465 AC: 1614 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.60
PhyloP100		1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1373302; hg19: chr8-72957716;