Variant rs3825842 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_144572.2(TBC1D2B):c.*1965C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.13 ( 0 hom., cov: 30)

Exomes 𝑓: 0.17 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

TBC1D2B
NM_144572.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.489

Variant links:

Genes affected

TBC1D2B (HGNC:29183): (TBC1 domain family member 2B) Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

TBC1D2B links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBC1D2B	NM_144572.2 linkuse as main transcript	c.*1965C>T		3_prime_UTR_variant	13/13	ENST00000300584.8	NP_653173.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBC1D2B	ENST00000300584.8 linkuse as main transcript	c.*1965C>T	3_prime_UTR_variant	13/13	5	NM_144572.2	ENSP00000300584	P1	Q9UPU7-1
TBC1D2B	ENST00000409931.7 linkuse as main transcript	c.*2060C>T	3_prime_UTR_variant	13/13	1		ENSP00000387165		Q9UPU7-2
TBC1D2B	ENST00000465531.1 linkuse as main transcript	c.66+5424C>T	intron_variant		4		ENSP00000453114
TBC1D2B	ENST00000418039.2 linkuse as main transcript	n.3187C>T	non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

16254

AN:

124976

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0468

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.102

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.0472

Gnomad SAS

AF:

0.134

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.102

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.135

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.167

AC:

AN:

Hom.:

Cov.:

AF XY:

0.167

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.167

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.130

AC:

16257

AN:

125106

Hom.:

Cov.:

AF XY:

0.131

AC XY:

8086

AN XY:

61782

show subpopulations

Gnomad4 AFR

AF:

0.0468

Gnomad4 AMR

AF:

0.102

Gnomad4 ASJ

AF:

0.163

Gnomad4 EAS

AF:

0.0469

Gnomad4 SAS

AF:

0.135

Gnomad4 FIN

AF:

0.160

Gnomad4 NFE

AF:

0.195

Gnomad4 OTH

AF:

0.133

Alfa

AF:

0.176

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.99

DANN

Benign

0.76

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over