rs10091803

chr8-72069626-G-Achr8-72069626-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007332.3(TRPA1):c.269-428C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 151,996 control chromosomes in the GnomAD database, including 2,441 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 0.16 (2441 hom., cov: 31)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPA1	NM_007332.3	c.269-428C>T		intron_variant		ENST00000262209.5
TRPA1	XM_011517624.3	c.344-428C>T		intron_variant
TRPA1	XM_011517625.3	c.269-428C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPA1	ENST00000262209.5	c.269-428C>T		intron_variant		1	NM_007332.3	P1
MSC-AS1	ENST00000518916.5	n.470-6895G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24525 AN: 151876 Hom.: 2435 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0892

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.161 AC: 24544 AN: 151996 Hom.: 2441 Cov.: 31 AF XY: 0.161 AC XY: 11927 AN XY: 74288

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.0890

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.156

Alfa AF: 0.0573 Hom.: 63

Bravo AF: 0.163

Asia WGS AF: 0.192 AC: 667 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	8.0
Dann	Benign	0.53

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

Publications

LitVar

Other links and lift over

dbSNP: rs10091803; hg19: chr8-72981861;