chr8-72059292-C-T

Variant names:

• chr8-72059292-C-T
• rs12548486
• NM_007332.3:c.993+98G>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.993+98G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 850,030 control chromosomes in the GnomAD database, including 58,661 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 0.37 (10958 hom., cov: 33)
  • Exomes 𝑓: 0.36 (47703 hom.)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 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.993+98G>A		intron	N/A	NP_015628.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPA1	ENST00000262209.5	TSL:1 MANE Select	c.993+98G>A		intron	N/A	ENSP00000262209.4
	TRPA1	ENST00000523582.5	TSL:5	c.549+98G>A		intron	N/A	ENSP00000428151.1
	MSC-AS1	ENST00000518916.5	TSL:3	n.469+6676C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56359 AN: 151810 Hom.: 10935 Cov.: 33

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.351

GnomAD4 exome AF: 0.362 AC: 252692 AN: 698102 Hom.: 47703 AF XY: 0.358 AC XY: 130563 AN XY: 364416

African (AFR) AF: 0.374 AC: 6062 AN: 16192

American (AMR) AF: 0.607 AC: 14756 AN: 24326

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 5086 AN: 18206

East Asian (EAS) AF: 0.553 AC: 17303 AN: 31302

South Asian (SAS) AF: 0.358 AC: 18506 AN: 51724

European-Finnish (FIN) AF: 0.418 AC: 18709 AN: 44762

Middle Eastern (MID) AF: 0.270 AC: 689 AN: 2548

European-Non Finnish (NFE) AF: 0.336 AC: 159478 AN: 475136

Other (OTH) AF: 0.357 AC: 12103 AN: 33906

GnomAD4 genome AF: 0.371 AC: 56422 AN: 151928 Hom.: 10958 Cov.: 33 AF XY: 0.377 AC XY: 27985 AN XY: 74224

African (AFR) AF: 0.369 AC: 15303 AN: 41438

American (AMR) AF: 0.505 AC: 7713 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 945 AN: 3470

East Asian (EAS) AF: 0.548 AC: 2834 AN: 5174

South Asian (SAS) AF: 0.356 AC: 1719 AN: 4830

European-Finnish (FIN) AF: 0.414 AC: 4352 AN: 10500

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22370 AN: 67940

Other (OTH) AF: 0.348 AC: 736 AN: 2112

Alfa AF: 0.248 Hom.: 616

Bravo AF: 0.383

Asia WGS AF: 0.464 AC: 1614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.5
DANN	Benign	0.40
PhyloP100		-1.1
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: rs12548486; hg19: chr8-72971527;