rs13255063

Variant names:

• chr8-72047300-T-A
• rs13255063
• NM_007332.3:c.1906-93A>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.1906-93A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 911,304 control chromosomes in the GnomAD database, including 26,519 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 0.20 (3564 hom., cov: 32)
  • Exomes 𝑓: 0.23 (22955 hom.)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 11 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPA1	NM_007332.3	c.1906-93A>T		intron_variant	Intron 15 of 26	ENST00000262209.5	NP_015628.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPA1	ENST00000262209.5	c.1906-93A>T		intron_variant	Intron 15 of 26	1	NM_007332.3	ENSP00000262209.4

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30847 AN: 151846 Hom.: 3564 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.0616

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.244

GnomAD4 exome AF: 0.235 AC: 178388 AN: 759340 Hom.: 22955 AF XY: 0.240 AC XY: 96784 AN XY: 402744

African (AFR) AF: 0.126 AC: 2425 AN: 19296

American (AMR) AF: 0.165 AC: 6298 AN: 38142

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 7967 AN: 20714

East Asian (EAS) AF: 0.0541 AC: 1927 AN: 35652

South Asian (SAS) AF: 0.259 AC: 17186 AN: 66482

European-Finnish (FIN) AF: 0.152 AC: 7823 AN: 51620

Middle Eastern (MID) AF: 0.368 AC: 1565 AN: 4252

European-Non Finnish (NFE) AF: 0.255 AC: 124218 AN: 486374

Other (OTH) AF: 0.244 AC: 8979 AN: 36808

GnomAD4 genome AF: 0.203 AC: 30863 AN: 151964 Hom.: 3564 Cov.: 32 AF XY: 0.200 AC XY: 14838 AN XY: 74306

African (AFR) AF: 0.125 AC: 5195 AN: 41486

American (AMR) AF: 0.204 AC: 3109 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1296 AN: 3470

East Asian (EAS) AF: 0.0623 AC: 323 AN: 5182

South Asian (SAS) AF: 0.236 AC: 1136 AN: 4812

European-Finnish (FIN) AF: 0.138 AC: 1455 AN: 10568

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17600 AN: 67898

Other (OTH) AF: 0.243 AC: 513 AN: 2108

Alfa AF: 0.226 Hom.: 537

Bravo AF: 0.201

Asia WGS AF: 0.139 AC: 486 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.75
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs13255063; hg19: chr8-72959535; COSMIC: COSV51557569; COSMIC: COSV51557569;