1-235379947-C-CA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_003193.5(TBCE):c.-31-55dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.72 (34119 hom., cov: 0)
  • Exomes 𝑓: 0.41 (1954 hom.)
  • Failed GnomAD Quality Control
• Consequence: TBCE NM_003193.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.566

Genes affected

TBCE (HGNC:11582): (tubulin folding cofactor E) Cofactor E 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. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-235379947-C-CA is Benign according to our data. Variant chr1-235379947-C-CA is described in ClinVar as [Benign]. Clinvar id is 1174300.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBCE	NM_003193.5	c.-31-55dup		intron_variant		ENST00000642610.2
TBCE	NM_001079515.3	c.-31-55dup		intron_variant
TBCE	NM_001287801.2	c.-31-55dup		intron_variant
TBCE	NM_001287802.2	c.-341-55dup		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBCE	ENST00000642610.2	c.-31-55dup		intron_variant			NM_003193.5	P1

Frequencies

GnomAD3 genomes AF: 0.721 AC: 95665 AN: 132642 Hom.: 34104 Cov.: 0

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.669

Gnomad OTH AF: 0.728

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.405 AC: 239520 AN: 590892 Hom.: 1954 AF XY: 0.404 AC XY: 125428 AN XY: 310450

Gnomad4 AFR exome AF: 0.457

Gnomad4 AMR exome AF: 0.397

Gnomad4 ASJ exome AF: 0.418

Gnomad4 EAS exome AF: 0.395

Gnomad4 SAS exome AF: 0.380

Gnomad4 FIN exome AF: 0.406

Gnomad4 NFE exome AF: 0.407

Gnomad4 OTH exome AF: 0.412

GnomAD4 genome AF: 0.721 AC: 95703 AN: 132672 Hom.: 34119 Cov.: 0 AF XY: 0.719 AC XY: 45339 AN XY: 63072

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.669

Gnomad4 OTH AF: 0.729

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Dec 04, 2020

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs36068852; hg19: chr1-235543262;