chr8-72065864-G-T

Variant names:

• chr8-72065864-G-T
• rs10104272
• NM_007332.3:c.445-306C>A

Variant summary

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

The NM_007332.3(TRPA1):​c.445-306C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 151,998 control chromosomes in the GnomAD database, including 37,069 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 0.69 (37069 hom., cov: 32)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPA1	NM_007332.3	c.445-306C>A		intron_variant	Intron 3 of 26	ENST00000262209.5	NP_015628.2
TRPA1	XM_011517624.3	c.520-306C>A		intron_variant	Intron 4 of 27		XP_011515926.1
TRPA1	XM_011517625.3	c.445-306C>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.445-306C>A		intron_variant	Intron 3 of 26	1	NM_007332.3	ENSP00000262209.4
MSC-AS1	ENST00000518916.5	n.470-10657G>T		intron_variant	Intron 3 of 6	3

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104606 AN: 151880 Hom.: 37024 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.689 AC: 104711 AN: 151998 Hom.: 37069 Cov.: 32 AF XY: 0.692 AC XY: 51450 AN XY: 74308

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.978

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.682

Alfa AF: 0.655 Hom.: 4091

Bravo AF: 0.703

Asia WGS AF: 0.834 AC: 2899 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.30

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: rs10104272; hg19: chr8-72978099;