rs13255063

chr8-72047300-T-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TRPA1	NM_007332.3	c.1906-93A>T		intron_variant		ENST00000262209.5
MSC-AS1	NR_033652.1	n.1029-5239T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPA1	ENST00000262209.5	c.1906-93A>T		intron_variant		1	NM_007332.3	P1
MSC-AS1	ENST00000518916.5	n.392-5239T>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR exome AF: 0.126

Gnomad4 AMR exome AF: 0.165

Gnomad4 ASJ exome AF: 0.385

Gnomad4 EAS exome AF: 0.0541

Gnomad4 SAS exome AF: 0.259

Gnomad4 FIN exome AF: 0.152

Gnomad4 NFE exome AF: 0.255

Gnomad4 OTH exome AF: 0.244

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

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.0623

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.243

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs13255063; hg19: chr8-72959535; COSMIC: COSV51557569; COSMIC: COSV51557569;