dbSNP rs10499110: TBC1D32:p.Gln102Gln (chr6-121321644-T-C) – ACMG Classification: Benign (-15 pts)

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_152730.6(TBC1D32):c.306A>G(p.Gln102Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0259 in 1,612,726 control chromosomes in the GnomAD database, including 1,876 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.052 ( 400 hom., cov: 32)

Exomes 𝑓: 0.023 ( 1476 hom. )

Consequence

TBC1D32
NM_152730.6 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0270

Variant links:

Genes affected

TBC1D32 (HGNC:21485): (TBC1 domain family member 32) This gene encodes a TBC-domain containing protein. Studies of a similar protein in mouse and zebrafish suggest that the encoded protein is involved in sonic hedgehog signaling, and that it interacts with and stabilizes cell cycle-related kinase. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

TBC1D32 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.63).

BP6

Variant 6-121321644-T-C is Benign according to our data. Variant chr6-121321644-T-C is described in ClinVar as [Benign]. Clinvar id is 1560549.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.027 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBC1D32	NM_152730.6 link	c.306A>G	p.Gln102Gln	synonymous_variant	Exon 2 of 32	ENST00000398212.7	NP_689943.4	Q96NH3-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
TBC1D32	ENST00000398212.7 link	c.306A>G	p.Gln102Gln	synonymous_variant	Exon 2 of 32	5	NM_152730.6	ENSP00000381270.2	Q96NH3-1
TBC1D32	ENST00000275159.11 link	c.306A>G	p.Gln102Gln	synonymous_variant	Exon 2 of 33	5		ENSP00000275159.6	Q96NH3-4
TBC1D32	ENST00000464622.5 link	n.306A>G		non_coding_transcript_exon_variant	Exon 2 of 36	2		ENSP00000428839.1	Q96NH3-5
TBC1D32	ENST00000422369.1 link	c.306A>G	p.Gln102Gln	synonymous_variant	Exon 3 of 6	3		ENSP00000397993.1	A2A304

Frequencies

GnomAD3 genomes

AF:

0.0515

AC:

7839

AN:

152114

Hom.:

400

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.0109

Gnomad EAS

AF:

0.117

Gnomad SAS

AF:

0.0128

Gnomad FIN

AF:

0.0291

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0132

Gnomad OTH

AF:

0.0483

GnomAD3 exomes

AF:

0.0491

AC:

12170

AN:

247982

Hom.:

822

AF XY:

0.0404

AC XY:

5434

AN XY:

134506

show subpopulations

Gnomad AFR exome

AF:

0.0994

Gnomad AMR exome

AF:

0.168

Gnomad ASJ exome

AF:

0.00918

Gnomad EAS exome

AF:

0.109

Gnomad SAS exome

AF:

0.00940

Gnomad FIN exome

AF:

0.0281

Gnomad NFE exome

AF:

0.0155

Gnomad OTH exome

AF:

0.0359

GnomAD4 exome

AF:

0.0232

AC:

33873

AN:

1460494

Hom.:

1476

Cov.:

AF XY:

0.0215

AC XY:

15638

AN XY:

726518

show subpopulations

Gnomad4 AFR exome

AF:

0.100

Gnomad4 AMR exome

AF:

0.159

Gnomad4 ASJ exome

AF:

0.0102

Gnomad4 EAS exome

AF:

0.144

Gnomad4 SAS exome

AF:

0.00985

Gnomad4 FIN exome

AF:

0.0290

Gnomad4 NFE exome

AF:

0.0121

Gnomad4 OTH exome

AF:

0.0267

GnomAD4 genome

AF:

0.0516

AC:

7850

AN:

152232

Hom.:

400

Cov.:

AF XY:

0.0528

AC XY:

3928

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.101

Gnomad4 AMR

AF:

0.108

Gnomad4 ASJ

AF:

0.0109

Gnomad4 EAS

AF:

0.117

Gnomad4 SAS

AF:

0.0124

Gnomad4 FIN

AF:

0.0291

Gnomad4 NFE

AF:

0.0132

Gnomad4 OTH

AF:

0.0497

Alfa

AF:

0.0282

Hom.:

Bravo

AF:

0.0631

Asia WGS

AF:

0.0880

AC:

306

AN:

3478

EpiCase

AF:

0.0114

EpiControl

AF:

0.0116

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jan 24, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

5.1

DANN

Benign

0.38

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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