Variant chr6-121091045-T-TA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_152730.6(TBC1D32):c.3466-5dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 1,224,990 control chromosomes in the GnomAD database, including 12,453 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 7362 hom., cov: 23)

Exomes 𝑓: 0.19 ( 5091 hom. )

Consequence

TBC1D32
NM_152730.6 splice_region, intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.424

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:

TBC1D32 (HGNC:):

TBC1D32 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 6-121091045-T-TA is Benign according to our data. Variant chr6-121091045-T-TA is described in ClinVar as [Benign]. Clinvar id is 1560532.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBC1D32	NM_152730.6 linkuse as main transcript	c.3466-5dupT		splice_region_variant, intron_variant		ENST00000398212.7	NP_689943.4	Q96NH3-1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
TBC1D32	ENST00000398212.7 linkuse as main transcript	c.3466-5dupT	splice_region_variant, intron_variant	5	NM_152730.6	ENSP00000381270.2	Q96NH3-1
TBC1D32	ENST00000275159.11 linkuse as main transcript	c.3589-5dupT	splice_region_variant, intron_variant	5		ENSP00000275159.6	Q96NH3-4
TBC1D32	ENST00000464622.5 linkuse as main transcript	n.*4106-5dupT	splice_region_variant, intron_variant	2		ENSP00000428839.1	Q96NH3-5

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

38878

AN:

147826

Hom.:

7341

Cov.:

show subpopulations

Gnomad AFR

AF:

0.527

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.313

Gnomad ASJ

AF:

0.141

Gnomad EAS

AF:

0.0987

Gnomad SAS

AF:

0.131

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.159

Gnomad NFE

AF:

0.143

Gnomad OTH

AF:

0.243

GnomAD3 exomes

AF:

0.255

AC:

34437

AN:

135180

Hom.:

1766

AF XY:

0.243

AC XY:

17690

AN XY:

72882

show subpopulations

Gnomad AFR exome

AF:

0.491

Gnomad AMR exome

AF:

0.415

Gnomad ASJ exome

AF:

0.239

Gnomad EAS exome

AF:

0.162

Gnomad SAS exome

AF:

0.245

Gnomad FIN exome

AF:

0.169

Gnomad NFE exome

AF:

0.203

Gnomad OTH exome

AF:

0.259

GnomAD4 exome

AF:

0.188

AC:

202427

AN:

1077080

Hom.:

5091

Cov.:

AF XY:

0.187

AC XY:

99713

AN XY:

534254

show subpopulations

Gnomad4 AFR exome

AF:

0.456

Gnomad4 AMR exome

AF:

0.357

Gnomad4 ASJ exome

AF:

0.182

Gnomad4 EAS exome

AF:

0.127

Gnomad4 SAS exome

AF:

0.183

Gnomad4 FIN exome

AF:

0.139

Gnomad4 NFE exome

AF:

0.178

Gnomad4 OTH exome

AF:

0.210

GnomAD4 genome

AF:

0.263

AC:

38944

AN:

147910

Hom.:

7362

Cov.:

AF XY:

0.260

AC XY:

18780

AN XY:

72098

show subpopulations

Gnomad4 AFR

AF:

0.528

Gnomad4 AMR

AF:

0.313

Gnomad4 ASJ

AF:

0.141

Gnomad4 EAS

AF:

0.0990

Gnomad4 SAS

AF:

0.131

Gnomad4 FIN

AF:

0.114

Gnomad4 NFE

AF:

0.143

Gnomad4 OTH

AF:

0.242

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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