chr8-72072076-T-C

Variant names:

• chr8-72072076-T-C
• rs4738205
• NM_007332.3:c.112-209A>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.112-209A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,012 control chromosomes in the GnomAD database, including 12,212 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 0.39 (12212 hom., cov: 32)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPA1	NM_007332.3	c.112-209A>G		intron_variant	Intron 1 of 26	ENST00000262209.5	NP_015628.2
TRPA1	XM_011517624.3	c.187-209A>G		intron_variant	Intron 2 of 27		XP_011515926.1
TRPA1	XM_011517625.3	c.112-209A>G		intron_variant	Intron 3 of 28		XP_011515927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPA1	ENST00000262209.5	c.112-209A>G		intron_variant	Intron 1 of 26	1	NM_007332.3	ENSP00000262209.4

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59232 AN: 151894 Hom.: 12181 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.390 AC: 59304 AN: 152012 Hom.: 12212 Cov.: 32 AF XY: 0.397 AC XY: 29472 AN XY: 74282

African (AFR) AF: 0.412 AC: 17056 AN: 41446

American (AMR) AF: 0.520 AC: 7944 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 946 AN: 3462

East Asian (EAS) AF: 0.631 AC: 3260 AN: 5170

South Asian (SAS) AF: 0.437 AC: 2106 AN: 4818

European-Finnish (FIN) AF: 0.414 AC: 4375 AN: 10564

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22390 AN: 67950

Other (OTH) AF: 0.366 AC: 773 AN: 2110

Alfa AF: 0.256 Hom.: 650

Bravo AF: 0.402

Asia WGS AF: 0.551 AC: 1914 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.56
PhyloP100		0.010
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: rs4738205; hg19: chr8-72984311;