rs2362293

chr2-233928209-G-T

Variant summary

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

The NM_024080.5(TRPM8):c.117+1555G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,580 control chromosomes in the GnomAD database, including 18,330 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 0.41 (18330 hom., cov: 30)
• Consequence: TRPM8 NM_024080.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

TRPM8 (HGNC:17961): (transient receptor potential cation channel subfamily M member 8) Predicted to enable ligand-gated calcium channel activity. Predicted to be involved in calcium ion transmembrane transport and positive regulation of cold-induced thermogenesis. Predicted to act upstream of or within several processes, including cellular calcium ion homeostasis; response to cold; and thermoception. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPM8	NM_024080.5	c.117+1555G>T		intron_variant		ENST00000324695.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRPM8	ENST00000324695.9	c.117+1555G>T		intron_variant		1	NM_024080.5	P1
TRPM8	ENST00000444298.5	c.117+1555G>T		intron_variant, NMD_transcript_variant		1
TRPM8	ENST00000433712.6	c.-607+1555G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62492 AN: 151462 Hom.: 18276 Cov.: 30

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.413 AC: 62620 AN: 151580 Hom.: 18330 Cov.: 30 AF XY: 0.414 AC XY: 30673 AN XY: 74090

Gnomad4 AFR AF: 0.806

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.362

Alfa AF: 0.318 Hom.: 1439

Bravo AF: 0.445

Asia WGS AF: 0.611 AC: 2123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.74
Dann	Benign	0.44

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: rs2362293; hg19: chr2-234836854;