8-72051023-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007332.3(TRPA1):c.1812-152A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 619,080 control chromosomes in the GnomAD database, including 120,348 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 0.63 (30405 hom., cov: 32)
  • Exomes 𝑓: 0.62 (89943 hom.)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPA1	NM_007332.3	c.1812-152A>G		intron_variant		ENST00000262209.5
MSC-AS1	NR_033652.1	n.1029-1516T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPA1	ENST00000262209.5	c.1812-152A>G		intron_variant		1	NM_007332.3	P1
MSC-AS1	ENST00000518916.5	n.392-1516T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95610 AN: 151922 Hom.: 30361 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.639

GnomAD4 exome AF: 0.616 AC: 287796 AN: 467038 Hom.: 89943 AF XY: 0.617 AC XY: 154290 AN XY: 249926

Gnomad4 AFR exome AF: 0.650

Gnomad4 AMR exome AF: 0.782

Gnomad4 ASJ exome AF: 0.653

Gnomad4 EAS exome AF: 0.669

Gnomad4 SAS exome AF: 0.666

Gnomad4 FIN exome AF: 0.573

Gnomad4 NFE exome AF: 0.589

Gnomad4 OTH exome AF: 0.626

GnomAD4 genome AF: 0.629 AC: 95704 AN: 152042 Hom.: 30405 Cov.: 32 AF XY: 0.632 AC XY: 46944 AN XY: 74308

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.636

Alfa AF: 0.598 Hom.: 50717

Bravo AF: 0.645

Asia WGS AF: 0.697 AC: 2426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.28
Dann	Benign	0.47

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: rs1025928; hg19: chr8-72963258;