chr8-72069349-C-T

Variant names:

• chr8-72069349-C-T
• rs1373297
• NM_007332.3:c.269-151G>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.269-151G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 771,652 control chromosomes in the GnomAD database, including 58,034 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 (12190 hom., cov: 32)
  • Exomes 𝑓: 0.37 (45844 hom.)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 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.269-151G>A		intron	N/A	NP_015628.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPA1	ENST00000262209.5	TSL:1 MANE Select	c.269-151G>A		intron	N/A	ENSP00000262209.4
	MSC-AS1	ENST00000518916.5	TSL:3	n.470-7172C>T		intron	N/A
	MSC-AS1	ENST00000767640.1		n.671+6984C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59157 AN: 151834 Hom.: 12162 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.367

GnomAD4 exome AF: 0.369 AC: 228952 AN: 619700 Hom.: 45844 AF XY: 0.367 AC XY: 120420 AN XY: 328394

African (AFR) AF: 0.402 AC: 6532 AN: 16236

American (AMR) AF: 0.616 AC: 18656 AN: 30300

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 4945 AN: 18324

East Asian (EAS) AF: 0.614 AC: 19959 AN: 32514

South Asian (SAS) AF: 0.407 AC: 23627 AN: 58032

European-Finnish (FIN) AF: 0.414 AC: 14445 AN: 34862

Middle Eastern (MID) AF: 0.268 AC: 728 AN: 2714

European-Non Finnish (NFE) AF: 0.325 AC: 128228 AN: 394632

Other (OTH) AF: 0.369 AC: 11832 AN: 32086

GnomAD4 genome AF: 0.390 AC: 59223 AN: 151952 Hom.: 12190 Cov.: 32 AF XY: 0.396 AC XY: 29445 AN XY: 74264

African (AFR) AF: 0.409 AC: 16959 AN: 41430

American (AMR) AF: 0.519 AC: 7931 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 948 AN: 3470

East Asian (EAS) AF: 0.630 AC: 3263 AN: 5176

South Asian (SAS) AF: 0.438 AC: 2109 AN: 4820

European-Finnish (FIN) AF: 0.415 AC: 4366 AN: 10516

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22422 AN: 67956

Other (OTH) AF: 0.366 AC: 772 AN: 2108

Alfa AF: 0.373 Hom.: 1395

Bravo AF: 0.402

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.65
PhyloP100		-0.50
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: rs1373297; hg19: chr8-72981584;