NM_007332.3:c.2937+403T>A

Variant names:

• chr8-72029498-A-T
• rs3824150
• NM_007332.3:c.2937+403T>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.2937+403T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 152,058 control chromosomes in the GnomAD database, including 11,573 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 0.38 (11573 hom., cov: 33)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.44
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 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.2937+403T>A		intron	N/A	NP_015628.2	O75762
	MSC-AS1	NR_033651.1		n.434-23041A>T		intron	N/A
	MSC-AS1	NR_033652.1		n.1029-23041A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPA1	ENST00000262209.5	TSL:1 MANE Select	c.2937+403T>A		intron	N/A	ENSP00000262209.4	O75762
	MSC-AS1	ENST00000457356.9	TSL:1	n.511-23041A>T		intron	N/A
	TRPA1	ENST00000859810.1		c.2937+403T>A		intron	N/A	ENSP00000529869.1

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57882 AN: 151940 Hom.: 11553 Cov.: 33

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.381 AC: 57945 AN: 152058 Hom.: 11573 Cov.: 33 AF XY: 0.387 AC XY: 28732 AN XY: 74334

African (AFR) AF: 0.403 AC: 16686 AN: 41444

American (AMR) AF: 0.509 AC: 7784 AN: 15286

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

East Asian (EAS) AF: 0.549 AC: 2838 AN: 5172

South Asian (SAS) AF: 0.356 AC: 1716 AN: 4826

European-Finnish (FIN) AF: 0.414 AC: 4372 AN: 10570

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22400 AN: 67976

Other (OTH) AF: 0.358 AC: 756 AN: 2110

Alfa AF: 0.368 Hom.: 1304

Bravo AF: 0.394

Asia WGS AF: 0.469 AC: 1631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.1
DANN	Benign	0.83
PhyloP100		2.4
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: rs3824150; hg19: chr8-72941733;