chr8-72043656-G-T

Variant names:

• chr8-72043656-G-T
• rs10504524
• NM_007332.3:c.2061+2857C>A

Variant summary

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

The NM_007332.3(TRPA1):​c.2061+2857C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,192 control chromosomes in the GnomAD database, including 4,901 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 0.25 (4901 hom., cov: 31)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPA1	NM_007332.3	c.2061+2857C>A		intron_variant	Intron 17 of 26	ENST00000262209.5	NP_015628.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPA1	ENST00000262209.5	c.2061+2857C>A		intron_variant	Intron 17 of 26	1	NM_007332.3	ENSP00000262209.4

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37544 AN: 151072 Hom.: 4900 Cov.: 31

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.249 AC: 37573 AN: 151192 Hom.: 4901 Cov.: 31 AF XY: 0.245 AC XY: 18119 AN XY: 73862

African (AFR) AF: 0.258 AC: 10624 AN: 41250

American (AMR) AF: 0.232 AC: 3515 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1303 AN: 3454

East Asian (EAS) AF: 0.145 AC: 747 AN: 5152

South Asian (SAS) AF: 0.318 AC: 1527 AN: 4802

European-Finnish (FIN) AF: 0.139 AC: 1448 AN: 10450

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17588 AN: 67624

Other (OTH) AF: 0.279 AC: 582 AN: 2088

Alfa AF: 0.235 Hom.: 2002

Bravo AF: 0.251

Asia WGS AF: 0.228 AC: 791 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.54
PhyloP100		-0.013
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: rs10504524; hg19: chr8-72955891;