chr8-72040923-C-T

Variant names:

• chr8-72040923-C-T
• rs1025926
• NM_007332.3:c.2062-1126G>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.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
• Publications: 5 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 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.2062-1126G>A		intron	N/A	NP_015628.2
	MSC-AS1	NR_033651.1		n.434-11616C>T		intron	N/A
	MSC-AS1	NR_033652.1		n.1029-11616C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPA1	ENST00000262209.5	TSL:1 MANE Select	c.2062-1126G>A		intron	N/A	ENSP00000262209.4
	MSC-AS1	ENST00000457356.9	TSL:1	n.511-11616C>T		intron	N/A
	TRPA1	ENST00000859810.1		c.2062-1126G>A		intron	N/A	ENSP00000529869.1

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

African (AFR) AF: 0.232 AC: 9601 AN: 41422

American (AMR) AF: 0.269 AC: 4091 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3466

East Asian (EAS) AF: 0.344 AC: 1775 AN: 5164

South Asian (SAS) AF: 0.136 AC: 654 AN: 4826

European-Finnish (FIN) AF: 0.340 AC: 3580 AN: 10544

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17037 AN: 67910

Other (OTH) AF: 0.233 AC: 491 AN: 2108

Alfa AF: 0.247 Hom.: 18622

Bravo AF: 0.250

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.7
DANN	Benign	0.28
PhyloP100		-0.56
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: rs1025926; hg19: chr8-72953158;