chr17-16422654-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_016113.5(TRPV2):ā€‹c.390A>Gā€‹(p.Gly130=) 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: š‘“ 0.45 ( 16074 hom., cov: 33)
Exomes š‘“: 0.39 ( 112092 hom. )

Consequence

TRPV2
NM_016113.5 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.781
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TRPV2NM_016113.5 linkuse as main transcriptc.390A>G p.Gly130= synonymous_variant 4/15 ENST00000338560.12 NP_057197.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TRPV2ENST00000338560.12 linkuse as main transcriptc.390A>G p.Gly130= synonymous_variant 4/151 NM_016113.5 ENSP00000342222 P1
TRPV2ENST00000455666.1 linkuse as main transcriptc.264A>G p.Gly88= synonymous_variant 3/43 ENSP00000390014

Frequencies

GnomAD3 genomes
AF:
0.446
AC:
67856
AN:
151976
Hom.:
16047
Cov.:
33
show subpopulations
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
GnomAD3 exomes
AF:
0.372
AC:
93023
AN:
250212
Hom.:
18408
AF XY:
0.364
AC XY:
49262
AN XY:
135242
show subpopulations
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 SAS exome
AF:
0.250
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
show subpopulations
Gnomad4 AFR exome
AF:
0.608
Gnomad4 AMR exome
AF:
0.326
Gnomad4 ASJ exome
AF:
0.415
Gnomad4 EAS exome
AF:
0.220
Gnomad4 SAS exome
AF:
0.255
Gnomad4 FIN exome
AF:
0.470
Gnomad4 NFE exome
AF:
0.393
Gnomad4 OTH exome
AF:
0.387
GnomAD4 genome
AF:
0.447
AC:
67941
AN:
152094
Hom.:
16074
Cov.:
33
AF XY:
0.443
AC XY:
32964
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.599
Gnomad4 AMR
AF:
0.371
Gnomad4 ASJ
AF:
0.440
Gnomad4 EAS
AF:
0.237
Gnomad4 SAS
AF:
0.254
Gnomad4 FIN
AF:
0.473
Gnomad4 NFE
AF:
0.400
Gnomad4 OTH
AF:
0.401
Alfa
AF:
0.402
Hom.:
20424
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 v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
4.1
DANN
Benign
0.51

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs8121; hg19: chr17-16325968; COSMIC: COSV58427735; COSMIC: COSV58427735; API