rs13280644

Variant names:

• chr8-72036353-C-T
• rs13280644
• NM_007332.3:c.2490G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6 BP7 BA1

The NM_007332.3(TRPA1):​c.2490G>A​(p.Leu830Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0898 in 1,613,898 control chromosomes in the GnomAD database, including 7,458 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.068 (526 hom., cov: 32)
  • Exomes 𝑓: 0.092 (6932 hom.)
• Consequence: TRPA1 NM_007332.3 synonymous
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.444
• Publications: 13 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BP6: Variant 8-72036353-C-T is Benign according to our data. Variant chr8-72036353-C-T is described in ClinVar as [Benign]. Clinvar id is 3056632.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP7: Synonymous conserved (PhyloP=0.444 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPA1	NM_007332.3	c.2490G>A	p.Leu830Leu	synonymous_variant	Exon 21 of 27	ENST00000262209.5	NP_015628.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPA1	ENST00000262209.5	c.2490G>A	p.Leu830Leu	synonymous_variant	Exon 21 of 27	1	NM_007332.3	ENSP00000262209.4

Frequencies

GnomAD3 genomes AF: 0.0685 AC: 10431 AN: 152168 Hom.: 527 Cov.: 32

Gnomad AFR AF: 0.0174

Gnomad AMI AF: 0.0507

Gnomad AMR AF: 0.0863

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0471

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0989

Gnomad OTH AF: 0.0876

GnomAD2 exomes AF: 0.0773 AC: 19404 AN: 251124 AF XY: 0.0826

Gnomad AFR exome AF: 0.0148

Gnomad AMR exome AF: 0.0598

Gnomad ASJ exome AF: 0.113

Gnomad EAS exome AF: 0.000435

Gnomad FIN exome AF: 0.0441

Gnomad NFE exome AF: 0.0964

Gnomad OTH exome AF: 0.0944

GnomAD4 exome AF: 0.0920 AC: 134503 AN: 1461612 Hom.: 6932 Cov.: 32 AF XY: 0.0935 AC XY: 67993 AN XY: 727112

African (AFR) AF: 0.0168 AC: 563 AN: 33478

American (AMR) AF: 0.0624 AC: 2792 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 2922 AN: 26130

East Asian (EAS) AF: 0.000327 AC: 13 AN: 39696

South Asian (SAS) AF: 0.112 AC: 9691 AN: 86240

European-Finnish (FIN) AF: 0.0454 AC: 2427 AN: 53416

Middle Eastern (MID) AF: 0.131 AC: 755 AN: 5768

European-Non Finnish (NFE) AF: 0.0990 AC: 110031 AN: 1111784

Other (OTH) AF: 0.0879 AC: 5309 AN: 60382

GnomAD4 genome AF: 0.0685 AC: 10430 AN: 152286 Hom.: 526 Cov.: 32 AF XY: 0.0673 AC XY: 5008 AN XY: 74464

African (AFR) AF: 0.0174 AC: 722 AN: 41578

American (AMR) AF: 0.0862 AC: 1319 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3460

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5184

South Asian (SAS) AF: 0.103 AC: 496 AN: 4824

European-Finnish (FIN) AF: 0.0471 AC: 500 AN: 10610

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0989 AC: 6724 AN: 68012

Other (OTH) AF: 0.0866 AC: 183 AN: 2112

Alfa AF: 0.0941 Hom.: 1493

Bravo AF: 0.0663

Asia WGS AF: 0.0510 AC: 176 AN: 3478

EpiCase AF: 0.102

EpiControl AF: 0.105

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

TRPA1-related disorder Benign:1

Oct 28, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	6.3
DANN	Benign	0.84
PhyloP100		0.44
Mutation Taster		=94/6	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: rs13280644; hg19: chr8-72948588;