8-72040923-C-T

Variant names:

• chr8-72040923-C-T
• rs1025926
• NM_007332.3:c.2062-1126G>A

Variant summary

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

The NM_007332.3(TRPA1):​c.2062-1126G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 151,876 control chromosomes in the GnomAD database, including 4,983 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 0.25 (4983 hom., cov: 32)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPA1	NM_007332.3	c.2062-1126G>A		intron_variant	Intron 17 of 26	ENST00000262209.5	NP_015628.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPA1	ENST00000262209.5	c.2062-1126G>A		intron_variant	Intron 17 of 26	1	NM_007332.3	ENSP00000262209.4

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38268 AN: 151758 Hom.: 4974 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.252 AC: 38315 AN: 151876 Hom.: 4983 Cov.: 32 AF XY: 0.255 AC XY: 18913 AN XY: 74224

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.233

Alfa AF: 0.241 Hom.: 8885

Bravo AF: 0.250

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.28

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: rs1025926; hg19: chr8-72953158;