8-72037366-C-T

Variant names:

• chr8-72037366-C-T
• rs11988795
• NM_007332.3:c.2385+617G>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.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
• Publications: 14 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 = 0.531 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPA1	NM_007332.3	MANE Select	c.2385+617G>A		intron	N/A	NP_015628.2
	MSC-AS1	NR_033651.1		n.434-15173C>T		intron	N/A
	MSC-AS1	NR_033652.1		n.1029-15173C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPA1	ENST00000262209.5	TSL:1 MANE Select	c.2385+617G>A		intron	N/A	ENSP00000262209.4
	MSC-AS1	ENST00000457356.9	TSL:1	n.511-15173C>T		intron	N/A
	TRPA1	ENST00000523582.5	TSL:5	c.1941+617G>A		intron	N/A	ENSP00000428151.1

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

African (AFR) AF: 0.361 AC: 14960 AN: 41400

American (AMR) AF: 0.504 AC: 7687 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3466

East Asian (EAS) AF: 0.548 AC: 2831 AN: 5170

South Asian (SAS) AF: 0.353 AC: 1702 AN: 4816

European-Finnish (FIN) AF: 0.415 AC: 4354 AN: 10486

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22329 AN: 67838

Other (OTH) AF: 0.348 AC: 736 AN: 2112

Alfa AF: 0.318 Hom.: 3883

Bravo AF: 0.381

Asia WGS AF: 0.460 AC: 1595 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.51
PhyloP100		-0.11
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: rs11988795; hg19: chr8-72949601;