chr8-72027391-G-C

Variant names:

• chr8-72027391-G-C
• rs13279503
• NM_007332.3:c.2938-1318C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.397 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.2938-1318C>G		intron	N/A	NP_015628.2
	MSC-AS1	NR_033651.1		n.434-25148G>C		intron	N/A
	MSC-AS1	NR_033652.1		n.1029-25148G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPA1	ENST00000262209.5	TSL:1 MANE Select	c.2938-1318C>G		intron	N/A	ENSP00000262209.4
	MSC-AS1	ENST00000457356.9	TSL:1	n.511-25148G>C		intron	N/A
	TRPA1	ENST00000523582.5	TSL:5	c.2494-1318C>G		intron	N/A	ENSP00000428151.1

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

African (AFR) AF: 0.203 AC: 8419 AN: 41480

American (AMR) AF: 0.269 AC: 4111 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1678 AN: 3470

East Asian (EAS) AF: 0.347 AC: 1789 AN: 5150

South Asian (SAS) AF: 0.412 AC: 1975 AN: 4794

European-Finnish (FIN) AF: 0.246 AC: 2605 AN: 10570

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24616 AN: 67958

Other (OTH) AF: 0.350 AC: 738 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.7
DANN	Benign	0.74
PhyloP100		0.61
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13279503; hg19: chr8-72939626;