rs1373297

Positions:

• chr8-72069349-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.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

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPA1	NM_007332.3	c.269-151G>A		intron_variant		ENST00000262209.5
TRPA1	XM_011517624.3	c.344-151G>A		intron_variant
TRPA1	XM_011517625.3	c.269-151G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPA1	ENST00000262209.5	c.269-151G>A		intron_variant		1	NM_007332.3	P1
MSC-AS1	ENST00000518916.5	n.470-7172C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR exome AF: 0.402

Gnomad4 AMR exome AF: 0.616

Gnomad4 ASJ exome AF: 0.270

Gnomad4 EAS exome AF: 0.614

Gnomad4 SAS exome AF: 0.407

Gnomad4 FIN exome AF: 0.414

Gnomad4 NFE exome AF: 0.325

Gnomad4 OTH exome AF: 0.369

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

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.415

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.366

Alfa AF: 0.371 Hom.: 1331

Bravo AF: 0.402

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.65

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: rs1373297; hg19: chr8-72981584;