rs4737338

Variant names:

• chr8-72049219-T-C
• rs4737338
• NM_007332.3:c.1905+1559A>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.1905+1559A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,976 control chromosomes in the GnomAD database, including 11,151 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 (11151 hom., cov: 33)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPA1	NM_007332.3	c.1905+1559A>G		intron_variant	Intron 15 of 26	ENST00000262209.5	NP_015628.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPA1	ENST00000262209.5	c.1905+1559A>G		intron_variant	Intron 15 of 26	1	NM_007332.3	ENSP00000262209.4

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56852 AN: 151858 Hom.: 11138 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.374 AC: 56900 AN: 151976 Hom.: 11151 Cov.: 33 AF XY: 0.380 AC XY: 28209 AN XY: 74250

African (AFR) AF: 0.379 AC: 15733 AN: 41466

American (AMR) AF: 0.508 AC: 7736 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 934 AN: 3468

East Asian (EAS) AF: 0.547 AC: 2821 AN: 5158

South Asian (SAS) AF: 0.356 AC: 1718 AN: 4828

European-Finnish (FIN) AF: 0.414 AC: 4366 AN: 10550

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22384 AN: 67950

Other (OTH) AF: 0.354 AC: 747 AN: 2112

Alfa AF: 0.365 Hom.: 1321

Bravo AF: 0.386

Asia WGS AF: 0.465 AC: 1617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.66
PhyloP100		-0.23
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: rs4737338; hg19: chr8-72961454;