Variant 12-64832208-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_015279.2(TBC1D30):c.498C>T(p.Ala166Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00653 in 1,536,098 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0055 ( 5 hom., cov: 33)

Exomes 𝑓: 0.0066 ( 43 hom. )

Consequence

TBC1D30
NM_015279.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.72

Variant links:

Genes affected

TBC1D30 (HGNC:29164): (TBC1 domain family member 30) Enables GTPase activator activity and small GTPase binding activity. Involved in negative regulation of cilium assembly and positive regulation of GTPase activity. Located in ciliary basal body; cytosol; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

TBC1D30 links:

ENSG00000288591 (HGNC:):

ENSG00000288591 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.23).

BP6

Variant 12-64832208-C-T is Benign according to our data. Variant chr12-64832208-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2643163.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.72 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBC1D30	NM_015279.2 linkuse as main transcript	c.498C>T	p.Ala166Ala	synonymous_variant	5/12	ENST00000539867.6	NP_056094.1	Q9Y2I9-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBC1D30	ENST00000539867.6 linkuse as main transcript	c.498C>T	p.Ala166Ala	synonymous_variant	5/12	1	NM_015279.2	ENSP00000440207.1		Q9Y2I9-2
ENSG00000288591	ENST00000674281.1 linkuse as main transcript	n.156C>T		non_coding_transcript_exon_variant	7/17			ENSP00000501395.1		F8VZ81

Frequencies

GnomAD3 genomes

AF:

0.00552

AC:

840

AN:

152168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000917

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.00412

Gnomad ASJ

AF:

0.0101

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00989

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00833

Gnomad OTH

AF:

0.00573

GnomAD3 exomes

AF:

0.00491

AC:

673

AN:

137072

Hom.:

AF XY:

0.00440

AC XY:

328

AN XY:

74526

show subpopulations

Gnomad AFR exome

AF:

0.000155

Gnomad AMR exome

AF:

0.00315

Gnomad ASJ exome

AF:

0.0104

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0138

Gnomad NFE exome

AF:

0.00732

Gnomad OTH exome

AF:

0.00476

GnomAD4 exome

AF:

0.00665

AC:

9196

AN:

1383812

Hom.:

Cov.:

AF XY:

0.00658

AC XY:

4495

AN XY:

682846

show subpopulations

Gnomad4 AFR exome

AF:

0.000950

Gnomad4 AMR exome

AF:

0.00314

Gnomad4 ASJ exome

AF:

0.00973

Gnomad4 EAS exome

AF:

0.0000280

Gnomad4 SAS exome

AF:

0.0000126

Gnomad4 FIN exome

AF:

0.0130

Gnomad4 NFE exome

AF:

0.00743

Gnomad4 OTH exome

AF:

0.00598

GnomAD4 genome

AF:

0.00552

AC:

840

AN:

152286

Hom.:

Cov.:

AF XY:

0.00545

AC XY:

406

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.000914

Gnomad4 AMR

AF:

0.00412

Gnomad4 ASJ

AF:

0.0101

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00989

Gnomad4 NFE

AF:

0.00833

Gnomad4 OTH

AF:

0.00567

Alfa

AF:

0.00880

Hom.:

Bravo

AF:

0.00482

Asia WGS

AF:

0.000289

AC:

AN:

3478

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

Nov 01, 2022

TBC1D30: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.23

CADD

Benign

9.2

DANN

Benign

0.67

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

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