1-235379947-CAAAAAAAAA-CAAAAAAA

Variant names:

• chr1-235379947-CAA-C
• rs36068852
• NM_003193.5:c.-31-56_-31-55delAA

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BS1

The NM_003193.5(TBCE):​c.-31-56_-31-55delAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00468 in 721,702 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000045 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0057 (0 hom.)
• Consequence: TBCE NM_003193.5 intron
• Clinical Significance: Not reported in ClinVar
• 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]

ENSG00000285053 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BS1: Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00572 (3371/588948) while in subpopulation AMR AF= 0.00692 (170/24578). AF 95% confidence interval is 0.00607. There are 0 homozygotes in gnomad4_exome. There are 1739 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBCE	NM_003193.5	c.-31-56_-31-55delAA		intron_variant	Intron 1 of 16	ENST00000642610.2	NP_003184.1
TBCE	NM_001287801.2	c.-31-56_-31-55delAA		intron_variant	Intron 1 of 17		NP_001274730.1
TBCE	NM_001079515.3	c.-31-56_-31-55delAA		intron_variant	Intron 1 of 16		NP_001072983.1
TBCE	NM_001287802.2	c.-341-56_-341-55delAA		intron_variant	Intron 1 of 15		NP_001274731.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBCE	ENST00000642610.2	c.-31-71_-31-70delAA		intron_variant	Intron 1 of 16		NM_003193.5	ENSP00000494796.1
ENSG00000285053	ENST00000645655.1	c.-31-71_-31-70delAA		intron_variant	Intron 4 of 19			ENSP00000495202.1

Frequencies

GnomAD3 genomes AF: 0.0000452 AC: 6 AN: 132754 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000556

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000280

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000322

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00572 AC: 3371 AN: 588948 Hom.: 0 AF XY: 0.00562 AC XY: 1739 AN XY: 309552

Gnomad4 AFR exome AF: 0.00371

Gnomad4 AMR exome AF: 0.00692

Gnomad4 ASJ exome AF: 0.00610

Gnomad4 EAS exome AF: 0.00631

Gnomad4 SAS exome AF: 0.00591

Gnomad4 FIN exome AF: 0.00650

Gnomad4 NFE exome AF: 0.00561

Gnomad4 OTH exome AF: 0.00581

GnomAD4 genome AF: 0.0000452 AC: 6 AN: 132754 Hom.: 0 Cov.: 0 AF XY: 0.0000159 AC XY: 1 AN XY: 63048

Gnomad4 AFR AF: 0.0000556

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000280

Gnomad4 NFE AF: 0.0000322

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

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;