Variant rs13936 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015043.4(TBC1D9B):c.*789C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 446,016 control chromosomes in the GnomAD database, including 6,627 homozygotes. 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 0.098 ( 1269 hom., cov: 33)

Exomes 𝑓: 0.15 ( 5358 hom. )

Consequence

TBC1D9B
NM_015043.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.159

Variant links:

Genes affected

TBC1D9B (HGNC:29097): (TBC1 domain family member 9B) Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TBC1D9B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBC1D9B	NM_015043.4 linkuse as main transcript	c.*789C>T		3_prime_UTR_variant	21/21	ENST00000355235.8	NP_055858.2
TBC1D9B	NM_198868.3 linkuse as main transcript	c.*789C>T		3_prime_UTR_variant	22/22		NP_942568.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBC1D9B	ENST00000355235.8 linkuse as main transcript	c.*789C>T		3_prime_UTR_variant	21/21	5	NM_015043.4	ENSP00000347375	A2	Q66K14-2

Frequencies

GnomAD3 genomes

AF:

0.0979

AC:

14901

AN:

152138

Hom.:

1264

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0194

Gnomad AMI

AF:

0.0526

Gnomad AMR

AF:

0.198

Gnomad ASJ

AF:

0.0847

Gnomad EAS

AF:

0.371

Gnomad SAS

AF:

0.278

Gnomad FIN

AF:

0.165

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0810

Gnomad OTH

AF:

0.0924

GnomAD4 exome

AF:

0.152

AC:

44610

AN:

293760

Hom.:

5358

Cov.:

AF XY:

0.159

AC XY:

26370

AN XY:

165496

show subpopulations

Gnomad4 AFR exome

AF:

0.0183

Gnomad4 AMR exome

AF:

0.350

Gnomad4 ASJ exome

AF:

0.0873

Gnomad4 EAS exome

AF:

0.354

Gnomad4 SAS exome

AF:

0.253

Gnomad4 FIN exome

AF:

0.158

Gnomad4 NFE exome

AF:

0.0795

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.0980

AC:

14914

AN:

152256

Hom.:

1269

Cov.:

AF XY:

0.108

AC XY:

8073

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.0193

Gnomad4 AMR

AF:

0.199

Gnomad4 ASJ

AF:

0.0847

Gnomad4 EAS

AF:

0.371

Gnomad4 SAS

AF:

0.277

Gnomad4 FIN

AF:

0.165

Gnomad4 NFE

AF:

0.0810

Gnomad4 OTH

AF:

0.100

Alfa

AF:

0.0991

Hom.:

872

Bravo

AF:

0.0986

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.2

DANN

Benign

0.58

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

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