chr8-72059292-C-T

Position:

• chr8-72059292-C-T

Variant summary

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

The NM_007332.3(TRPA1):​c.993+98G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 850,030 control chromosomes in the GnomAD database, including 58,661 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 0.37 (10958 hom., cov: 33)
  • Exomes 𝑓: 0.36 (47703 hom.)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRPA1	NM_007332.3	c.993+98G>A		intron_variant		ENST00000262209.5	NP_015628.2
TRPA1	XM_011517624.3	c.1068+98G>A		intron_variant			XP_011515926.1
TRPA1	XM_011517625.3	c.993+98G>A		intron_variant			XP_011515927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRPA1	ENST00000262209.5	c.993+98G>A		intron_variant		1	NM_007332.3	ENSP00000262209.4
TRPA1	ENST00000523582.5	c.549+98G>A		intron_variant		5		ENSP00000428151.1
MSC-AS1	ENST00000518916.5	n.469+6676C>T		intron_variant		3
MSC-AS1	ENST00000519068.3	n.449-1071C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56359 AN: 151810 Hom.: 10935 Cov.: 33

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.351

GnomAD4 exome AF: 0.362 AC: 252692 AN: 698102 Hom.: 47703 AF XY: 0.358 AC XY: 130563 AN XY: 364416

Gnomad4 AFR exome AF: 0.374

Gnomad4 AMR exome AF: 0.607

Gnomad4 ASJ exome AF: 0.279

Gnomad4 EAS exome AF: 0.553

Gnomad4 SAS exome AF: 0.358

Gnomad4 FIN exome AF: 0.418

Gnomad4 NFE exome AF: 0.336

Gnomad4 OTH exome AF: 0.357

GnomAD4 genome AF: 0.371 AC: 56422 AN: 151928 Hom.: 10958 Cov.: 33 AF XY: 0.377 AC XY: 27985 AN XY: 74224

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.348

Alfa AF: 0.240 Hom.: 571

Bravo AF: 0.383

Asia WGS AF: 0.464 AC: 1614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.5
DANN	Benign	0.40

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: rs12548486; hg19: chr8-72971527;