chr8-72068417-C-T

Variant names:

• chr8-72068417-C-T
• rs1443952
• NM_007332.3:c.444+606G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007332.3(TRPA1):​c.444+606G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,002 control chromosomes in the GnomAD database, including 10,457 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 0.36 (10457 hom., cov: 32)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 8 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPA1	NM_007332.3	c.444+606G>A		intron_variant	Intron 3 of 26	ENST00000262209.5	NP_015628.2
TRPA1	XM_011517624.3	c.519+606G>A		intron_variant	Intron 4 of 27		XP_011515926.1
TRPA1	XM_011517625.3	c.444+606G>A		intron_variant	Intron 5 of 28		XP_011515927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPA1	ENST00000262209.5	c.444+606G>A		intron_variant	Intron 3 of 26	1	NM_007332.3	ENSP00000262209.4

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54959 AN: 151884 Hom.: 10441 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.362 AC: 55006 AN: 152002 Hom.: 10457 Cov.: 32 AF XY: 0.368 AC XY: 27344 AN XY: 74282

African (AFR) AF: 0.337 AC: 13950 AN: 41446

American (AMR) AF: 0.502 AC: 7667 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 933 AN: 3466

East Asian (EAS) AF: 0.548 AC: 2829 AN: 5158

South Asian (SAS) AF: 0.355 AC: 1712 AN: 4816

European-Finnish (FIN) AF: 0.414 AC: 4376 AN: 10574

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22367 AN: 67956

Other (OTH) AF: 0.342 AC: 720 AN: 2106

Alfa AF: 0.353 Hom.: 8069

Bravo AF: 0.372

Asia WGS AF: 0.462 AC: 1606 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	4.6
DANN	Benign	0.56
PhyloP100		0.056
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1443952; hg19: chr8-72980652;