Variant 17-79942150-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_019020.4(TBC1D16):c.1965C>T(p.Asp655=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00175 in 1,610,084 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0013 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0018 ( 9 hom. )

Consequence

TBC1D16
NM_019020.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.44

Variant links:

Genes affected

TBC1D16 (HGNC:28356): (TBC1 domain family member 16) Enables GTPase activator activity. Involved in regulation of receptor recycling. Located in cytosol and early endosome. [provided by Alliance of Genome Resources, Apr 2022]

TBC1D16 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 17-79942150-G-A is Benign according to our data. Variant chr17-79942150-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2648391.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.44 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBC1D16	NM_019020.4 linkuse as main transcript	c.1965C>T	p.Asp655=	synonymous_variant	11/12	ENST00000310924.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBC1D16	ENST00000310924.7 linkuse as main transcript	c.1965C>T	p.Asp655=	synonymous_variant	11/12	1	NM_019020.4	P1	Q8TBP0-1
TBC1D16	ENST00000340848.11 linkuse as main transcript	c.879C>T	p.Asp293=	synonymous_variant	7/8	1			Q8TBP0-2
TBC1D16	ENST00000576768.5 linkuse as main transcript	c.840C>T	p.Asp280=	synonymous_variant	7/8	1			Q8TBP0-4

Frequencies

GnomAD3 genomes

AF:

0.00128

AC:

195

AN:

152164

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000458

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.000982

Gnomad ASJ

AF:

0.00750

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00186

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00178

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00142

AC:

346

AN:

242978

Hom.:

AF XY:

0.00159

AC XY:

210

AN XY:

131690

show subpopulations

Gnomad AFR exome

AF:

0.000457

Gnomad AMR exome

AF:

0.000529

Gnomad ASJ exome

AF:

0.00792

Gnomad EAS exome

AF:

0.0000553

Gnomad SAS exome

AF:

0.00215

Gnomad FIN exome

AF:

0.0000481

Gnomad NFE exome

AF:

0.00150

Gnomad OTH exome

AF:

0.00235

GnomAD4 exome

AF:

0.00180

AC:

2623

AN:

1457802

Hom.:

Cov.:

AF XY:

0.00184

AC XY:

1330

AN XY:

724796

show subpopulations

Gnomad4 AFR exome

AF:

0.000269

Gnomad4 AMR exome

AF:

0.000631

Gnomad4 ASJ exome

AF:

0.00883

Gnomad4 EAS exome

AF:

0.0000253

Gnomad4 SAS exome

AF:

0.00227

Gnomad4 FIN exome

AF:

0.0000766

Gnomad4 NFE exome

AF:

0.00181

Gnomad4 OTH exome

AF:

0.00216

GnomAD4 genome

AF:

0.00128

AC:

195

AN:

152282

Hom.:

Cov.:

AF XY:

0.00117

AC XY:

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.000457

Gnomad4 AMR

AF:

0.000980

Gnomad4 ASJ

AF:

0.00750

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00186

Gnomad4 FIN

AF:

0.0000942

Gnomad4 NFE

AF:

0.00178

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00218

Hom.:

Bravo

AF:

0.00136

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2022

TBC1D16: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.14

DANN

Benign

0.93

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