8-72037366-C-T

Position:

• chr8-72037366-C-T

Variant summary

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

The NM_007332.3(TRPA1):​c.2385+617G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,730 control chromosomes in the GnomAD database, including 10,813 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 0.37 (10813 hom., cov: 32)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

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:):

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 = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRPA1	NM_007332.3	c.2385+617G>A		intron_variant		ENST00000262209.5	NP_015628.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRPA1	ENST00000262209.5	c.2385+617G>A		intron_variant		1	NM_007332.3	ENSP00000262209.4

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55935 AN: 151612 Hom.: 10791 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.369 AC: 55997 AN: 151730 Hom.: 10813 Cov.: 32 AF XY: 0.375 AC XY: 27810 AN XY: 74148

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.348

Alfa AF: 0.303 Hom.: 2106

Bravo AF: 0.381

Asia WGS AF: 0.460 AC: 1595 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.51

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: rs11988795; hg19: chr8-72949601;