chr8-72074553-C-T

Position:

• chr8-72074553-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.111+746G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,932 control chromosomes in the GnomAD database, including 12,122 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 (12122 hom., cov: 32)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.96

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=-0.87).
• 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/exons	MANE	Protein	UniProt
TRPA1	NM_007332.3	c.111+746G>A		intron_variant		ENST00000262209.5	NP_015628.2
TRPA1	XM_011517624.3	c.186+746G>A		intron_variant			XP_011515926.1
TRPA1	XM_011517625.3	c.111+746G>A		intron_variant			XP_011515927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRPA1	ENST00000262209.5	c.111+746G>A		intron_variant		1	NM_007332.3	ENSP00000262209	P1
MSC-AS1	ENST00000518916.5	n.470-1968C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.389 AC: 58994 AN: 151814 Hom.: 12090 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.389 AC: 59067 AN: 151932 Hom.: 12122 Cov.: 32 AF XY: 0.395 AC XY: 29362 AN XY: 74252

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.366

Alfa AF: 0.369 Hom.: 1321

Bravo AF: 0.401

Asia WGS AF: 0.551 AC: 1918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.67
DANN	Benign	0.77

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: rs10111216; hg19: chr8-72986788;