Variant chr10-47064-ACCTCCTCCTCGGCATACTCCTCATCCT-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_177987.3(TUBB8):c.1301_1327delAGGATGAGGAGTATGCCGAGGAGGAGG(p.Glu434_Glu442del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000939 in 1,117,948 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00011 ( 0 hom., cov: 21)

Exomes 𝑓: 0.000091 ( 0 hom. )

Consequence

TUBB8
NM_177987.3 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.65

Variant links:

Genes affected

TUBB8 (HGNC:20773): (tubulin beta 8 class VIII) The protein encoded by this gene represents the primary beta-tubulin subunit of oocytes and the early embryo. Defects in this gene, which is primate-specific, are a cause of oocyte maturation defect 2 and infertility. [provided by RefSeq, Mar 2016]

TUBB8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUBB8	NM_177987.3 link	c.1301_1327delAGGATGAGGAGTATGCCGAGGAGGAGG	p.Glu434_Glu442del	disruptive_inframe_deletion	4/4	ENST00000568584.6	NP_817124.1	Q3ZCM7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TUBB8	ENST00000568584.6 link	c.1301_1327delAGGATGAGGAGTATGCCGAGGAGGAGG	p.Glu434_Glu442del	disruptive_inframe_deletion	4/4	1	NM_177987.3	ENSP00000456206.2	Q3ZCM7
TUBB8	ENST00000564130.2 link	c.1199_1225delAGGATGAGGAGTATGCCGAGGAGGAGG	p.Glu400_Glu408del	disruptive_inframe_deletion	4/4	5		ENSP00000457610.1	Q5SQY0
TUBB8	ENST00000568866.5 link	c.1190_1216delAGGATGAGGAGTATGCCGAGGAGGAGG	p.Glu397_Glu405del	disruptive_inframe_deletion	3/3	5		ENSP00000457062.1	A0A075B736
TUBB8	ENST00000561967 link	c.964_990delAGGATGAGGAGTATGCCGAGGAGGAGG		3_prime_UTR_variant	4/4	5		ENSP00000454878.1	A0A075B724

Frequencies

GnomAD3 genomes

AF:

0.000111

AC:

AN:

143790

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000105

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000704

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000167

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000687

AC:

AN:

174636

Hom.:

AF XY:

0.0000642

AC XY:

AN XY:

93488

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000137

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0000712

Gnomad NFE exome

AF:

0.0000920

Gnomad OTH exome

AF:

0.000436

GnomAD4 exome

AF:

0.0000914

AC:

AN:

974158

Hom.:

AF XY:

0.0000821

AC XY:

AN XY:

499504

show subpopulations

Gnomad4 AFR exome

AF:

0.0000823

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.0000467

Gnomad4 EAS exome

AF:

0.0000814

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0000645

Gnomad4 NFE exome

AF:

0.000109

Gnomad4 OTH exome

AF:

0.0000906

GnomAD4 genome

AF:

0.000111

AC:

AN:

143790

Hom.:

Cov.:

AF XY:

0.000115

AC XY:

AN XY:

69510

show subpopulations

Gnomad4 AFR

AF:

0.000105

Gnomad4 AMR

AF:

0.0000704

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000167

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000480

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over