rs13279503

chr8-72027391-G-Cchr8-72027391-G-T

Variant summary

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

The NM_007332.3(TRPA1):c.2938-1318C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,016 control chromosomes in the GnomAD database, including 7,523 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 0.30 (7523 hom., cov: 32)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.609

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPA1	NM_007332.3	c.2938-1318C>G		intron_variant		ENST00000262209.5
MSC-AS1	NR_033652.1	n.1029-25148G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPA1	ENST00000262209.5	c.2938-1318C>G		intron_variant		1	NM_007332.3	P1
MSC-AS1	ENST00000518916.5	n.392-25148G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46256 AN: 151898 Hom.: 7525 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.304 AC: 46280 AN: 152016 Hom.: 7523 Cov.: 32 AF XY: 0.303 AC XY: 22512 AN XY: 74296

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.350

Alfa AF: 0.180 Hom.: 391

Bravo AF: 0.296

Asia WGS AF: 0.317 AC: 1104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.7
Dann	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs13279503; hg19: chr8-72939626;