Genetic Variant TBCA:c.160-902T>C (chr5-77694254-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_004607.3(TBCA):c.160-902T>C 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 152,036 control chromosomes in the GnomAD database, including 24,276 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 0.56 ( 24276 hom., cov: 33)

Failed GnomAD Quality Control

Consequence

TBCA
NM_004607.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.83

Publications

1 publications found

Variant links:

Genes affected

TBCA (HGNC:11579): (tubulin folding cofactor A) The product of this gene 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. This gene encodes chaperonin cofactor A. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]

TBCA links:

ENSG00000305113 (HGNC:):

ENSG00000305113 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.32).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004607.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TBCA	NM_004607.3	MANE Select	c.160-902T>C	intron	N/A	NP_004598.1
TBCA	NM_001297738.2		c.160-902T>C	intron	N/A	NP_001284667.1
TBCA	NM_001297740.2		c.160-2756T>C	intron	N/A	NP_001284669.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TBCA	ENST00000380377.9	TSL:1 MANE Select	c.160-902T>C	intron	N/A	ENSP00000369736.4
TBCA	ENST00000517881.1	TSL:2	n.24T>C	non_coding_transcript_exon	Exon 1 of 3
TBCA	ENST00000518338.6	TSL:2	c.229-902T>C	intron	N/A	ENSP00000429793.2

Frequencies

GnomAD3 genomes

AF:

0.563

AC:

85495

AN:

151918

Hom.:

24260

Cov.:

show subpopulations

Gnomad AFR

AF:

0.614

Gnomad AMI

AF:

0.579

Gnomad AMR

AF:

0.501

Gnomad ASJ

AF:

0.683

Gnomad EAS

AF:

0.468

Gnomad SAS

AF:

0.662

Gnomad FIN

AF:

0.518

Gnomad MID

AF:

0.585

Gnomad NFE

AF:

0.546

Gnomad OTH

AF:

0.583

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.563

AC:

85558

AN:

152036

Hom.:

24276

Cov.:

AF XY:

0.563

AC XY:

41868

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.614

AC:

25444

AN:

41466

American (AMR)

AF:

0.500

AC:

7637

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.683

AC:

2370

AN:

3468

East Asian (EAS)

AF:

0.470

AC:

2425

AN:

5162

South Asian (SAS)

AF:

0.661

AC:

3182

AN:

4814

European-Finnish (FIN)

AF:

0.518

AC:

5465

AN:

10556

Middle Eastern (MID)

AF:

0.582

AC:

171

AN:

294

European-Non Finnish (NFE)

AF:

0.546

AC:

37108

AN:

67988

Other (OTH)

AF:

0.582

AC:

1229

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1924

3848

5771

7695

9619

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

736

1472

2208

2944

3680

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.549

Hom.:

2963

Bravo

AF:

0.561

Asia WGS

AF:

0.560

AC:

1945

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.32

CADD

Benign

(source)

DANN

Benign

0.82

PhyloP100

2.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over