rs4737338

Positions:

• chr8-72049219-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TRPA1	NM_007332.3	c.1905+1559A>G		intron_variant		ENST00000262209.5
MSC-AS1	NR_033652.1	n.1029-3320T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPA1	ENST00000262209.5	c.1905+1559A>G		intron_variant		1	NM_007332.3	P1
MSC-AS1	ENST00000518916.5	n.392-3320T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.354

Alfa AF: 0.364 Hom.: 1272

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs4737338; hg19: chr8-72961454;