rs2587562

Positions:

• chr8-72078803-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011517624.3(TRPA1):​c.23-3341C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,758 control chromosomes in the GnomAD database, including 15,240 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 0.44 (15240 hom., cov: 32)
• Consequence: TRPA1 XM_011517624.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRPA1	XM_011517624.3	c.23-3341C>T		intron_variant			XP_011515926.1
TRPA1	XM_011517625.3	c.-54+2373C>T		intron_variant			XP_011515927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSC-AS1	ENST00000518916.5	n.576+2176G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67333 AN: 151640 Hom.: 15224 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.444 AC: 67377 AN: 151758 Hom.: 15240 Cov.: 32 AF XY: 0.444 AC XY: 32928 AN XY: 74158

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.463

Alfa AF: 0.447 Hom.: 24687

Bravo AF: 0.432

Asia WGS AF: 0.371 AC: 1287 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.45
DANN	Benign	0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2587562; hg19: chr8-72991038;