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

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1

The NM_152730.6(TBC1D32):c.3466-5delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00942 in 1,216,078 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00049 ( 0 hom., cov: 23)

Exomes 𝑓: 0.011 ( 0 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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP6

Variant 6-121091045-TA-T is Benign according to our data. Variant chr6-121091045-TA-T is described in ClinVar as [Benign]. Clinvar id is 1601435.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.0107 (11385/1068194) while in subpopulation SAS AF= 0.0202 (1145/56578). AF 95% confidence interval is 0.0193. There are 0 homozygotes in gnomad4_exome. There are 5912 alleles in male gnomad4_exome subpopulation. Median coverage is 29. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBC1D32	NM_152730.6 linkuse as main transcript	c.3466-5delT		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.3466-5delT	splice_region_variant, intron_variant	5	NM_152730.6	ENSP00000381270.2	Q96NH3-1
TBC1D32	ENST00000275159.11 linkuse as main transcript	c.3589-5delT	splice_region_variant, intron_variant	5		ENSP00000275159.6	Q96NH3-4
TBC1D32	ENST00000464622.5 linkuse as main transcript	n.*4106-5delT	splice_region_variant, intron_variant	2		ENSP00000428839.1	Q96NH3-5

Frequencies

GnomAD3 genomes

AF:

0.000494

AC:

AN:

147800

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000443

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000202

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00314

Gnomad SAS

AF:

0.000214

Gnomad FIN

AF:

0.00117

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000346

Gnomad OTH

AF:

0.000497

GnomAD3 exomes

AF:

0.0184

AC:

2492

AN:

135180

Hom.:

AF XY:

0.0193

AC XY:

1407

AN XY:

72882

show subpopulations

Gnomad AFR exome

AF:

0.00273

Gnomad AMR exome

AF:

0.0142

Gnomad ASJ exome

AF:

0.0416

Gnomad EAS exome

AF:

0.0220

Gnomad SAS exome

AF:

0.0296

Gnomad FIN exome

AF:

0.0218

Gnomad NFE exome

AF:

0.0176

Gnomad OTH exome

AF:

0.0202

GnomAD4 exome

AF:

0.0107

AC:

11385

AN:

1068194

Hom.:

Cov.:

AF XY:

0.0112

AC XY:

5912

AN XY:

528776

show subpopulations

Gnomad4 AFR exome

AF:

0.00282

Gnomad4 AMR exome

AF:

0.00968

Gnomad4 ASJ exome

AF:

0.0160

Gnomad4 EAS exome

AF:

0.0112

Gnomad4 SAS exome

AF:

0.0202

Gnomad4 FIN exome

AF:

0.0141

Gnomad4 NFE exome

AF:

0.0100

Gnomad4 OTH exome

AF:

0.0107

GnomAD4 genome

AF:

0.000494

AC:

AN:

147884

Hom.:

Cov.:

AF XY:

0.000500

AC XY:

AN XY:

72066

show subpopulations

Gnomad4 AFR

AF:

0.000442

Gnomad4 AMR

AF:

0.000201

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00315

Gnomad4 SAS

AF:

0.000215

Gnomad4 FIN

AF:

0.00117

Gnomad4 NFE

AF:

0.000346

Gnomad4 OTH

AF:

0.000493

Alfa

AF:

0.00614

Hom.:

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

Jul 17, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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