chr17-16422654-A-G

Variant names:

• chr17-16422654-A-G
• rs8121
• NM_016113.5:c.390A>G

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_016113.5(TRPV2):​c.390A>G​(p.Gly130Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 1,613,554 control chromosomes in the GnomAD database, including 128,166 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 0.45 (16074 hom., cov: 33)
  • Exomes 𝑓: 0.39 (112092 hom.)
• Consequence: TRPV2 NM_016113.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.781
• Publications: 29 publications found

Genes affected

TRPV2 (HGNC:18082): (transient receptor potential cation channel subfamily V member 2) This gene encodes an ion channel that is activated by high temperatures above 52 degrees Celsius. The protein may be involved in transduction of high-temperature heat responses in sensory ganglia. It is thought that in other tissues the channel may be activated by stimuli other than heat. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.004).
• BP7: Synonymous conserved (PhyloP=-0.781 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016113.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPV2	NM_016113.5	MANE Select	c.390A>G	p.Gly130Gly	synonymous	Exon 4 of 15	NP_057197.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPV2	ENST00000338560.12	TSL:1 MANE Select	c.390A>G	p.Gly130Gly	synonymous	Exon 4 of 15	ENSP00000342222.7
	TRPV2	ENST00000455666.1	TSL:3	c.261A>G	p.Gly87Gly	synonymous	Exon 3 of 4	ENSP00000390014.1

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67856 AN: 151976 Hom.: 16047 Cov.: 33

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.399

GnomAD2 exomes AF: 0.372 AC: 93023 AN: 250212 AF XY: 0.364

Gnomad AFR exome AF: 0.603

Gnomad AMR exome AF: 0.320

Gnomad ASJ exome AF: 0.418

Gnomad EAS exome AF: 0.230

Gnomad FIN exome AF: 0.470

Gnomad NFE exome AF: 0.387

Gnomad OTH exome AF: 0.382

GnomAD4 exome AF: 0.386 AC: 564414 AN: 1461460 Hom.: 112092 Cov.: 53 AF XY: 0.382 AC XY: 277725 AN XY: 726986

African (AFR) AF: 0.608 AC: 20347 AN: 33474

American (AMR) AF: 0.326 AC: 14572 AN: 44668

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 10844 AN: 26126

East Asian (EAS) AF: 0.220 AC: 8726 AN: 39684

South Asian (SAS) AF: 0.255 AC: 21988 AN: 86220

European-Finnish (FIN) AF: 0.470 AC: 25077 AN: 53384

Middle Eastern (MID) AF: 0.359 AC: 2067 AN: 5760

European-Non Finnish (NFE) AF: 0.393 AC: 437449 AN: 1111766

Other (OTH) AF: 0.387 AC: 23344 AN: 60378

GnomAD4 genome AF: 0.447 AC: 67941 AN: 152094 Hom.: 16074 Cov.: 33 AF XY: 0.443 AC XY: 32964 AN XY: 74354

African (AFR) AF: 0.599 AC: 24864 AN: 41484

American (AMR) AF: 0.371 AC: 5663 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1526 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1227 AN: 5172

South Asian (SAS) AF: 0.254 AC: 1225 AN: 4828

European-Finnish (FIN) AF: 0.473 AC: 5008 AN: 10578

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27201 AN: 67966

Other (OTH) AF: 0.401 AC: 847 AN: 2114

Alfa AF: 0.406 Hom.: 27703

Bravo AF: 0.444

Asia WGS AF: 0.260 AC: 905 AN: 3478

EpiCase AF: 0.395

EpiControl AF: 0.386

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.51
PhyloP100		-0.78
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.10		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: rs8121; hg19: chr17-16325968; COSMIC: COSV58427735; COSMIC: COSV58427735;