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GeneBe

11-122777123-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_032873.5(UBASH3B):c.315C>T(p.Ser105=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00389 in 1,614,072 control chromosomes in the GnomAD database, including 219 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.021 ( 109 hom., cov: 32)
Exomes 𝑓: 0.0021 ( 110 hom. )

Consequence

UBASH3B
NM_032873.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -6.09
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-122777123-C-T is Benign according to our data. Variant chr11-122777123-C-T is described in ClinVar as [Benign]. Clinvar id is 781236.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-6.09 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0703 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
UBASH3BNM_032873.5 linkuse as main transcriptc.315C>T p.Ser105= synonymous_variant 3/14 ENST00000284273.6
UBASH3BNM_001363365.2 linkuse as main transcriptc.210C>T p.Ser70= synonymous_variant 3/14
UBASH3BXM_005271712.4 linkuse as main transcriptc.399C>T p.Ser133= synonymous_variant 3/14
UBASH3BXM_011543041.3 linkuse as main transcriptc.258C>T p.Ser86= synonymous_variant 3/14

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
UBASH3BENST00000284273.6 linkuse as main transcriptc.315C>T p.Ser105= synonymous_variant 3/141 NM_032873.5 P1
ENST00000649590.1 linkuse as main transcriptn.74-11074G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0206
AC:
3137
AN:
152110
Hom.:
109
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0725
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00583
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000827
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000191
Gnomad OTH
AF:
0.0134
GnomAD3 exomes
AF:
0.00530
AC:
1333
AN:
251320
Hom.:
41
AF XY:
0.00404
AC XY:
549
AN XY:
135840
show subpopulations
Gnomad AFR exome
AF:
0.0723
Gnomad AMR exome
AF:
0.00347
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000462
Gnomad NFE exome
AF:
0.000211
Gnomad OTH exome
AF:
0.00212
GnomAD4 exome
AF:
0.00215
AC:
3136
AN:
1461844
Hom.:
110
Cov.:
30
AF XY:
0.00184
AC XY:
1337
AN XY:
727228
show subpopulations
Gnomad4 AFR exome
AF:
0.0758
Gnomad4 AMR exome
AF:
0.00382
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000696
Gnomad4 FIN exome
AF:
0.0000374
Gnomad4 NFE exome
AF:
0.000112
Gnomad4 OTH exome
AF:
0.00460
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0206
AC:
3143
AN:
152228
Hom.:
109
Cov.:
32
AF XY:
0.0204
AC XY:
1516
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.0725
Gnomad4 AMR
AF:
0.00582
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000621
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000191
Gnomad4 OTH
AF:
0.0133
Alfa
AF:
0.00948
Hom.:
16
Bravo
AF:
0.0228
Asia WGS
AF:
0.00375
AC:
13
AN:
3478
EpiCase
AF:
0.000218
EpiControl
AF:
0.000119

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJun 29, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
Cadd
Benign
0.22
Dann
Benign
0.78

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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.

Other links and lift over

dbSNP: rs35380329; hg19: chr11-122647831; API