Variant chr11-122656113-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000284273.6(UBASH3B):c.64G>C(p.Val22Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.003 in 1,600,994 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0026 ( 1 hom., cov: 31)

Exomes 𝑓: 0.0030 ( 13 hom. )

Consequence

UBASH3B
ENST00000284273.6 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.17

Variant links:

Genes affected

UBASH3B (HGNC:29884): (ubiquitin associated and SH3 domain containing B) This gene encodes a protein that contains a ubiquitin associated domain at the N-terminus, an SH3 domain, and a C-terminal domain with similarities to the catalytic motif of phosphoglycerate mutase. The encoded protein was found to inhibit endocytosis of epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor. [provided by RefSeq, Jul 2008]

UBASH3B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005106777).

BP6

Variant 11-122656113-G-C is Benign according to our data. Variant chr11-122656113-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2642480.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 389 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBASH3B	NM_032873.5 linkuse as main transcript	c.64G>C	p.Val22Leu	missense_variant	1/14	ENST00000284273.6	NP_116262.2
UBASH3B	NM_001363365.2 linkuse as main transcript	c.-46G>C		5_prime_UTR_variant	1/14		NP_001350294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBASH3B	ENST00000284273.6 linkuse as main transcript	c.64G>C	p.Val22Leu	missense_variant	1/14	1	NM_032873.5	ENSP00000284273	P1
UBASH3B	ENST00000525711.1 linkuse as main transcript	n.389G>C		non_coding_transcript_exon_variant	1/2	4

Frequencies

GnomAD3 genomes

AF:

0.00256

AC:

389

AN:

152176

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000844

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000523

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00452

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00428

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00241

AC:

532

AN:

220510

Hom.:

AF XY:

0.00246

AC XY:

297

AN XY:

120782

show subpopulations

Gnomad AFR exome

AF:

0.000471

Gnomad AMR exome

AF:

0.000308

Gnomad ASJ exome

AF:

0.000108

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000644

Gnomad FIN exome

AF:

0.00431

Gnomad NFE exome

AF:

0.00418

Gnomad OTH exome

AF:

0.00185

GnomAD4 exome

AF:

0.00305

AC:

4418

AN:

1448700

Hom.:

Cov.:

AF XY:

0.00302

AC XY:

2174

AN XY:

719884

show subpopulations

Gnomad4 AFR exome

AF:

0.000275

Gnomad4 AMR exome

AF:

0.000343

Gnomad4 ASJ exome

AF:

0.000155

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000856

Gnomad4 FIN exome

AF:

0.00522

Gnomad4 NFE exome

AF:

0.00355

Gnomad4 OTH exome

AF:

0.00192

GnomAD4 genome

AF:

0.00255

AC:

389

AN:

152294

Hom.:

Cov.:

AF XY:

0.00246

AC XY:

183

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.000842

Gnomad4 AMR

AF:

0.000523

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000621

Gnomad4 FIN

AF:

0.00452

Gnomad4 NFE

AF:

0.00428

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00166

Hom.:

Bravo

AF:

0.00195

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.00363

AC:

ESP6500AA

AF:

0.000685

AC:

ESP6500EA

AF:

0.00419

AC:

ExAC

AF:

0.00247

AC:

298

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

Jul 01, 2022

UBASH3B: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.50

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Benign

0.95

DEOGEN2

Benign

0.030

Eigen

Benign

-0.19

Eigen_PC

Benign

-0.080

FATHMM_MKL

Uncertain

0.83

LIST_S2

Uncertain

0.89

M_CAP

Benign

0.051

MetaRNN

Benign

0.0051

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.97

MutationTaster

Benign

0.97

PrimateAI

Pathogenic

0.79

PROVEAN

Benign

-0.040

REVEL

Benign

0.030

Sift

Benign

0.14

Sift4G

Benign

0.60

Polyphen

0.54

Vest4

0.32

MVP

0.15

MPC

0.47

ClinPred

0.020

GERP RS

3.4

Varity_R

0.084

gMVP

0.38

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