Variant rs3744161 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005993.5(TBCD):c.1319-43G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 1,609,494 control chromosomes in the GnomAD database, including 258,531 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.52 ( 21529 hom., cov: 33)

Exomes 𝑓: 0.57 ( 237002 hom. )

Consequence

TBCD
NM_005993.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.484

Variant links:

Genes affected

TBCD (HGNC:11581): (tubulin folding cofactor D) Cofactor D is one of four proteins (cofactors A, D, E, and C) involved in the pathway leading to correctly folded beta-tubulin from folding intermediates. Cofactors A and D are believed to play a role in capturing and stabilizing beta-tubulin intermediates in a quasi-native confirmation. Cofactor E binds to the cofactor D/beta-tubulin complex; interaction with cofactor C then causes the release of beta-tubulin polypeptides that are committed to the native state. [provided by RefSeq, Jul 2008]

TBCD links:

LOC124904096 (HGNC:):

LOC124904096 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 17-82870181-G-A is Benign according to our data. Variant chr17-82870181-G-A is described in ClinVar as [Benign]. Clinvar id is 1265397.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBCD	NM_005993.5 link	c.1319-43G>A		intron_variant		ENST00000355528.9	NP_005984.3	Q9BTW9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBCD	ENST00000355528.9 link	c.1319-43G>A		intron_variant		1	NM_005993.5	ENSP00000347719.4		Q9BTW9-1

Frequencies

GnomAD3 genomes

AF:

0.522

AC:

79274

AN:

151930

Hom.:

21511

Cov.:

show subpopulations

Gnomad AFR

AF:

0.364

Gnomad AMI

AF:

0.752

Gnomad AMR

AF:

0.587

Gnomad ASJ

AF:

0.512

Gnomad EAS

AF:

0.710

Gnomad SAS

AF:

0.463

Gnomad FIN

AF:

0.602

Gnomad MID

AF:

0.456

Gnomad NFE

AF:

0.578

Gnomad OTH

AF:

0.535

GnomAD3 exomes

AF:

0.563

AC:

137718

AN:

244402

Hom.:

39715

AF XY:

0.558

AC XY:

74335

AN XY:

133232

show subpopulations

Gnomad AFR exome

AF:

0.355

Gnomad AMR exome

AF:

0.628

Gnomad ASJ exome

AF:

0.517

Gnomad EAS exome

AF:

0.727

Gnomad SAS exome

AF:

0.463

Gnomad FIN exome

AF:

0.595

Gnomad NFE exome

AF:

0.573

Gnomad OTH exome

AF:

0.556

GnomAD4 exome

AF:

0.567

AC:

826919

AN:

1457446

Hom.:

237002

Cov.:

AF XY:

0.565

AC XY:

409692

AN XY:

725248

show subpopulations

Gnomad4 AFR exome

AF:

0.352

Gnomad4 AMR exome

AF:

0.617

Gnomad4 ASJ exome

AF:

0.516

Gnomad4 EAS exome

AF:

0.741

Gnomad4 SAS exome

AF:

0.464

Gnomad4 FIN exome

AF:

0.592

Gnomad4 NFE exome

AF:

0.575

Gnomad4 OTH exome

AF:

0.552

GnomAD4 genome

AF:

0.522

AC:

79335

AN:

152048

Hom.:

21529

Cov.:

AF XY:

0.524

AC XY:

38975

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.364

Gnomad4 AMR

AF:

0.587

Gnomad4 ASJ

AF:

0.512

Gnomad4 EAS

AF:

0.710

Gnomad4 SAS

AF:

0.465

Gnomad4 FIN

AF:

0.602

Gnomad4 NFE

AF:

0.578

Gnomad4 OTH

AF:

0.539

Alfa

AF:

0.484

Hom.:

2648

Bravo

AF:

0.516

Asia WGS

AF:

0.542

AC:

1887

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 15, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.4

DANN

Benign

0.75

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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