rs10101155

Variant names:

• chr8-72059782-C-A
• rs10101155
• NM_007332.3:c.945-344G>T

Your query was ambiguous. Multiple possible variants found:

• chr8-72059782-C-A
• chr8-72059782-C-G

Variant summary

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

The NM_007332.3(TRPA1):​c.945-344G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,918 control chromosomes in the GnomAD database, including 12,294 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 0.39 (12294 hom., cov: 32)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 2 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPA1	NM_007332.3	c.945-344G>T		intron_variant	Intron 7 of 26	ENST00000262209.5	NP_015628.2
TRPA1	XM_011517624.3	c.1020-344G>T		intron_variant	Intron 8 of 27		XP_011515926.1
TRPA1	XM_011517625.3	c.945-344G>T		intron_variant	Intron 9 of 28		XP_011515927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPA1	ENST00000262209.5	c.945-344G>T		intron_variant	Intron 7 of 26	1	NM_007332.3	ENSP00000262209.4

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59412 AN: 151800 Hom.: 12264 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.392 AC: 59483 AN: 151918 Hom.: 12294 Cov.: 32 AF XY: 0.398 AC XY: 29543 AN XY: 74254

African (AFR) AF: 0.417 AC: 17254 AN: 41422

American (AMR) AF: 0.521 AC: 7956 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 944 AN: 3464

East Asian (EAS) AF: 0.631 AC: 3261 AN: 5170

South Asian (SAS) AF: 0.437 AC: 2106 AN: 4820

European-Finnish (FIN) AF: 0.415 AC: 4360 AN: 10518

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22384 AN: 67936

Other (OTH) AF: 0.365 AC: 767 AN: 2102

Alfa AF: 0.354 Hom.: 27356

Bravo AF: 0.404

Asia WGS AF: 0.551 AC: 1916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.087
DANN	Benign	0.32
PhyloP100		-1.2
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: rs10101155; hg19: chr8-72972017;