8-72065200-T-A

Variant names:

• chr8-72065200-T-A
• rs12677736
• NM_007332.3:c.552+251A>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_007332.3(TRPA1):​c.552+251A>T 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 151,984 control chromosomes in the GnomAD database, including 12,211 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 (12211 hom., cov: 32)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007332.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPA1	NM_007332.3	MANE Select	c.552+251A>T		intron	N/A	NP_015628.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPA1	ENST00000262209.5	TSL:1 MANE Select	c.552+251A>T		intron	N/A	ENSP00000262209.4
	TRPA1	ENST00000859810.1		c.552+251A>T		intron	N/A	ENSP00000529869.1
	TRPA1	ENST00000523582.5	TSL:5	c.108+251A>T		intron	N/A	ENSP00000428151.1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59222 AN: 151866 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: 0.631

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.415

Gnomad MID AF: 0.234

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: 59293 AN: 151984 Hom.: 12211 Cov.: 32 AF XY: 0.397 AC XY: 29475 AN XY: 74282

African (AFR) AF: 0.411 AC: 17049 AN: 41442

American (AMR) AF: 0.520 AC: 7929 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3466

East Asian (EAS) AF: 0.631 AC: 3260 AN: 5164

South Asian (SAS) AF: 0.436 AC: 2104 AN: 4822

European-Finnish (FIN) AF: 0.415 AC: 4384 AN: 10554

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22396 AN: 67966

Other (OTH) AF: 0.366 AC: 771 AN: 2104

Alfa AF: 0.361 Hom.: 1251

Bravo AF: 0.402

Asia WGS AF: 0.551 AC: 1917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	9.1
DANN	Benign	0.90
PhyloP100		0.021
PromoterAI		-0.0040	Neutral
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: rs12677736; hg19: chr8-72977435;