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GeneBe

16-4874333-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001079514.3(UBN1):c.1923C>T(p.Leu641=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0101 in 1,614,182 control chromosomes in the GnomAD database, including 114 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0082 ( 11 hom., cov: 33)
Exomes 𝑓: 0.010 ( 103 hom. )

Consequence

UBN1
NM_001079514.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.651
Variant links:
Genes affected
UBN1 (HGNC:12506): (ubinuclein 1) Cellular senescence is a hallmark of tumor suppression and tissue aging. Senescent cells contain domains of heterochromatin, called senescence-associated heterochromatin foci (SAHF), that repress proliferation-promoting genes. The protein encoded by this gene binds to proliferation-promoting genes and is required for SAHF formation, enhancing methylation of histone H3. [provided by RefSeq, Oct 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 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=-0.7).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 16-4874333-C-T is Benign according to our data. Variant chr16-4874333-C-T is described in ClinVar as [Benign]. Clinvar id is 781182.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=0.651 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 11 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
UBN1NM_001079514.3 linkuse as main transcriptc.1923C>T p.Leu641= synonymous_variant 15/18 ENST00000262376.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
UBN1ENST00000262376.11 linkuse as main transcriptc.1923C>T p.Leu641= synonymous_variant 15/181 NM_001079514.3 P4Q9NPG3-1
UBN1ENST00000396658.8 linkuse as main transcriptc.1923C>T p.Leu641= synonymous_variant 14/171 P4Q9NPG3-1
UBN1ENST00000590769.5 linkuse as main transcriptc.1923C>T p.Leu641= synonymous_variant 15/172 A1Q9NPG3-2
UBN1ENST00000586716.1 linkuse as main transcriptc.303C>T p.Leu101= synonymous_variant 4/43

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00822
AC:
1251
AN:
152216
Hom.:
11
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00200
Gnomad AMI
AF:
0.00219
Gnomad AMR
AF:
0.00498
Gnomad ASJ
AF:
0.00461
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00373
Gnomad FIN
AF:
0.0250
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0114
Gnomad OTH
AF:
0.00525
GnomAD3 exomes
AF:
0.00840
AC:
2112
AN:
251416
Hom.:
19
AF XY:
0.00883
AC XY:
1200
AN XY:
135894
show subpopulations
Gnomad AFR exome
AF:
0.00148
Gnomad AMR exome
AF:
0.00304
Gnomad ASJ exome
AF:
0.00536
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00438
Gnomad FIN exome
AF:
0.0242
Gnomad NFE exome
AF:
0.0106
Gnomad OTH exome
AF:
0.0101
GnomAD4 exome
AF:
0.0103
AC:
15084
AN:
1461848
Hom.:
103
Cov.:
31
AF XY:
0.0102
AC XY:
7431
AN XY:
727228
show subpopulations
Gnomad4 AFR exome
AF:
0.00146
Gnomad4 AMR exome
AF:
0.00369
Gnomad4 ASJ exome
AF:
0.00486
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.00512
Gnomad4 FIN exome
AF:
0.0219
Gnomad4 NFE exome
AF:
0.0113
Gnomad4 OTH exome
AF:
0.00927
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00823
AC:
1253
AN:
152334
Hom.:
11
Cov.:
33
AF XY:
0.00847
AC XY:
631
AN XY:
74486
show subpopulations
Gnomad4 AFR
AF:
0.00200
Gnomad4 AMR
AF:
0.00503
Gnomad4 ASJ
AF:
0.00461
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00394
Gnomad4 FIN
AF:
0.0250
Gnomad4 NFE
AF:
0.0114
Gnomad4 OTH
AF:
0.00520
Alfa
AF:
0.00847
Hom.:
6
Bravo
AF:
0.00669
Asia WGS
AF:
0.00173
AC:
6
AN:
3478
EpiCase
AF:
0.0112
EpiControl
AF:
0.00859

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 13, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.70
Cadd
Benign
4.3
Dann
Benign
0.68
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.2

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.

Other links and lift over

dbSNP: rs143954303; hg19: chr16-4924334; API