chr8-72074553-C-T

Variant names:

• chr8-72074553-C-T
• rs10111216
• NM_007332.3:c.111+746G>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.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
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 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.111+746G>A		intron	N/A	NP_015628.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPA1	ENST00000262209.5	TSL:1 MANE Select	c.111+746G>A		intron	N/A	ENSP00000262209.4
	TRPA1	ENST00000859810.1		c.111+746G>A		intron	N/A	ENSP00000529869.1
	MSC-AS1	ENST00000518916.5	TSL:3	n.470-1968C>T		intron	N/A

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

African (AFR) AF: 0.411 AC: 17019 AN: 41402

American (AMR) AF: 0.519 AC: 7928 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 946 AN: 3468

East Asian (EAS) AF: 0.631 AC: 3254 AN: 5160

South Asian (SAS) AF: 0.437 AC: 2106 AN: 4822

European-Finnish (FIN) AF: 0.410 AC: 4328 AN: 10556

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.328 AC: 22261 AN: 67946

Other (OTH) AF: 0.366 AC: 771 AN: 2108

Alfa AF: 0.371 Hom.: 1384

Bravo AF: 0.401

Asia WGS AF: 0.551 AC: 1918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.67
DANN	Benign	0.77
PhyloP100		-3.0
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: rs10111216; hg19: chr8-72986788;