rs10091803

Variant names:

• chr8-72069626-G-A
• rs10091803
• NM_007332.3:c.269-428C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-72069626-G-A
• chr8-72069626-G-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.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
• Publications: 0 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007332.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPA1	NM_007332.3	MANE Select	c.269-428C>T		intron	N/A	NP_015628.2	O75762

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPA1	ENST00000262209.5	TSL:1 MANE Select	c.269-428C>T		intron	N/A	ENSP00000262209.4	O75762
	TRPA1	ENST00000859810.1		c.269-428C>T		intron	N/A	ENSP00000529869.1
	MSC-AS1	ENST00000518916.5	TSL:3	n.470-6895G>A		intron	N/A

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

African (AFR) AF: 0.275 AC: 11411 AN: 41426

American (AMR) AF: 0.0890 AC: 1359 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 488 AN: 3470

East Asian (EAS) AF: 0.286 AC: 1474 AN: 5162

South Asian (SAS) AF: 0.180 AC: 865 AN: 4816

European-Finnish (FIN) AF: 0.110 AC: 1163 AN: 10554

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7347 AN: 67978

Other (OTH) AF: 0.156 AC: 329 AN: 2110

Alfa AF: 0.0671 Hom.: 92

Bravo AF: 0.163

Asia WGS AF: 0.192 AC: 667 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.0
DANN	Benign	0.53
PhyloP100		0.024
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: rs10091803; hg19: chr8-72981861;