rs2052029

Variant names:

• chr2-234019044-C-G
• rs2052029
• NM_024080.5:c.*1788C>G

Your query was ambiguous. Multiple possible variants found:

• chr2-234019044-C-G
• chr2-234019044-C-T

Variant summary

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

The NM_024080.5(TRPM8):​c.*1788C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 151,876 control chromosomes in the GnomAD database, including 42,692 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 0.75 (42692 hom., cov: 30)
  • Failed GnomAD Quality Control
• Consequence: TRPM8 NM_024080.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.791
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPM8	NM_024080.5	c.*1788C>G		3_prime_UTR_variant	Exon 26 of 26	ENST00000324695.9	NP_076985.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPM8	ENST00000324695.9	c.*1788C>G		3_prime_UTR_variant	Exon 26 of 26	1	NM_024080.5	ENSP00000323926.4
TRPM8	ENST00000433712.6	c.*1788C>G		3_prime_UTR_variant	Exon 24 of 24	5		ENSP00000404423.3

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113127 AN: 151758 Hom.: 42637 Cov.: 30

Gnomad AFR AF: 0.846

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.750

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.746 AC: 113241 AN: 151876 Hom.: 42692 Cov.: 30 AF XY: 0.748 AC XY: 55508 AN XY: 74230

African (AFR) AF: 0.847 AC: 35077 AN: 41430

American (AMR) AF: 0.804 AC: 12269 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2400 AN: 3468

East Asian (EAS) AF: 0.811 AC: 4195 AN: 5172

South Asian (SAS) AF: 0.666 AC: 3211 AN: 4820

European-Finnish (FIN) AF: 0.699 AC: 7324 AN: 10476

Middle Eastern (MID) AF: 0.740 AC: 216 AN: 292

European-Non Finnish (NFE) AF: 0.681 AC: 46244 AN: 67940

Other (OTH) AF: 0.750 AC: 1582 AN: 2110

Alfa AF: 0.618 Hom.: 1683

Bravo AF: 0.758

Asia WGS AF: 0.735 AC: 2555 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.62
DANN	Benign	0.66
PhyloP100		-0.79
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: rs2052029; hg19: chr2-234927688;