chr8-72043656-G-T

Position:

• chr8-72043656-G-T

Variant summary

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

The NM_007332.3(TRPA1):​c.2061+2857C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,192 control chromosomes in the GnomAD database, including 4,901 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 0.25 (4901 hom., cov: 31)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRPA1	NM_007332.3	c.2061+2857C>A		intron_variant		ENST00000262209.5	NP_015628.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRPA1	ENST00000262209.5	c.2061+2857C>A		intron_variant		1	NM_007332.3	ENSP00000262209.4

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37544 AN: 151072 Hom.: 4900 Cov.: 31

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.249 AC: 37573 AN: 151192 Hom.: 4901 Cov.: 31 AF XY: 0.245 AC XY: 18119 AN XY: 73862

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.279

Alfa AF: 0.231 Hom.: 1705

Bravo AF: 0.251

Asia WGS AF: 0.228 AC: 791 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.54

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: rs10504524; hg19: chr8-72955891;