Variant 17-15628628-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001348119.1(TRIM16):c.1682G>T(p.Gly561Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 1,607,676 control chromosomes in the GnomAD database, including 48,021 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.23 ( 4119 hom., cov: 31)

Exomes 𝑓: 0.24 ( 43902 hom. )

Consequence

TRIM16
NM_001348119.1 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.439

Variant links:

Genes affected

TRIM16 (HGNC:17241): (tripartite motif containing 16) The protein encoded by this gene is a tripartite motif (TRIM) family member that contains two B box domains and a coiled-coiled region that are characteristic of the B box zinc finger protein family. While it lacks a RING domain found in other TRIM proteins, the encoded protein can homodimerize or heterodimerize with other TRIM proteins and has E3 ubiquitin ligase activity. This gene is also a tumor suppressor and is involved in secretory autophagy. [provided by RefSeq, Jan 2017]

TRIM16 links:

ENSG00000251537 (HGNC:):

ENSG00000251537 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004581034).

BP6

Variant 17-15628628-C-A is Benign according to our data. Variant chr17-15628628-C-A is described in ClinVar as [Benign]. Clinvar id is 770442.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM16	NM_001348119.1 linkuse as main transcript	c.1682G>T	p.Gly561Val	missense_variant	12/12	ENST00000649191.2	NP_001335048.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM16	ENST00000649191.2 linkuse as main transcript	c.1682G>T	p.Gly561Val	missense_variant	12/12		NM_001348119.1	ENSP00000497185.2		O95361-1
ENSG00000251537	ENST00000455584.2 linkuse as main transcript	c.1283+399G>T		intron_variant		2		ENSP00000402644.2		H0Y626

Frequencies

GnomAD3 genomes

AF:

0.229

AC:

34695

AN:

151822

Hom.:

4112

Cov.:

show subpopulations

Gnomad AFR

AF:

0.174

Gnomad AMI

AF:

0.202

Gnomad AMR

AF:

0.267

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.314

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.207

Gnomad NFE

AF:

0.248

Gnomad OTH

AF:

0.229

GnomAD3 exomes

AF:

0.247

AC:

58703

AN:

237998

Hom.:

7403

AF XY:

0.246

AC XY:

31757

AN XY:

129044

show subpopulations

Gnomad AFR exome

AF:

0.175

Gnomad AMR exome

AF:

0.295

Gnomad ASJ exome

AF:

0.177

Gnomad EAS exome

AF:

0.326

Gnomad SAS exome

AF:

0.272

Gnomad FIN exome

AF:

0.213

Gnomad NFE exome

AF:

0.235

Gnomad OTH exome

AF:

0.229

GnomAD4 exome

AF:

0.245

AC:

356061

AN:

1455734

Hom.:

43902

Cov.:

AF XY:

0.245

AC XY:

177244

AN XY:

723774

show subpopulations

Gnomad4 AFR exome

AF:

0.176

Gnomad4 AMR exome

AF:

0.296

Gnomad4 ASJ exome

AF:

0.173

Gnomad4 EAS exome

AF:

0.276

Gnomad4 SAS exome

AF:

0.273

Gnomad4 FIN exome

AF:

0.219

Gnomad4 NFE exome

AF:

0.245

Gnomad4 OTH exome

AF:

0.243

GnomAD4 genome

AF:

0.229

AC:

34720

AN:

151942

Hom.:

4119

Cov.:

AF XY:

0.228

AC XY:

16964

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.174

Gnomad4 AMR

AF:

0.268

Gnomad4 ASJ

AF:

0.175

Gnomad4 EAS

AF:

0.313

Gnomad4 SAS

AF:

0.274

Gnomad4 FIN

AF:

0.219

Gnomad4 NFE

AF:

0.248

Gnomad4 OTH

AF:

0.227

Alfa

AF:

0.188

Hom.:

685

Bravo

AF:

0.229

ExAC

AF:

0.238

AC:

28829

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Apr 17, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.089

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.57

CADD

Benign

0.66

DANN

Benign

0.73

DEOGEN2

Benign

0.0060

.;.;T;T;T

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.054

LIST_S2

Benign

0.28

T;T;.;T;.

MetaRNN

Benign

0.0046

T;T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.0

.;.;N;N;N

PROVEAN

Benign

-0.93

.;N;.;N;.

REVEL

Benign

0.051

Sift

Benign

0.083

.;T;.;T;.

Sift4G

Benign

0.16

T;T;T;T;.

Polyphen

0.037, 0.0040

.;B;B;B;B

Vest4

0.050

MPC

0.17

ClinPred

0.00071

GERP RS

0.87

Varity_R

0.035

gMVP

0.20

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over