chr16-4874279-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001079514.3(UBN1):c.1869G>C(p.Leu623Phe) variant causes a missense change. The variant allele was found at a frequency of 0.000361 in 1,613,490 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0018 ( 3 hom., cov: 33)
Exomes 𝑓: 0.00021 ( 1 hom. )
Consequence
UBN1
NM_001079514.3 missense
NM_001079514.3 missense
Scores
1
4
13
Clinical Significance
Conservation
PhyloP100: 6.21
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0066578686).
BP6
?
Variant 16-4874279-G-C is Benign according to our data. Variant chr16-4874279-G-C is described in ClinVar as [Benign]. Clinvar id is 727127.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 3 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UBN1 | NM_001079514.3 | c.1869G>C | p.Leu623Phe | missense_variant | 15/18 | ENST00000262376.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UBN1 | ENST00000262376.11 | c.1869G>C | p.Leu623Phe | missense_variant | 15/18 | 1 | NM_001079514.3 | P4 | |
UBN1 | ENST00000396658.8 | c.1869G>C | p.Leu623Phe | missense_variant | 14/17 | 1 | P4 | ||
UBN1 | ENST00000590769.5 | c.1869G>C | p.Leu623Phe | missense_variant | 15/17 | 2 | A1 | ||
UBN1 | ENST00000586716.1 | c.249G>C | p.Leu83Phe | missense_variant | 4/4 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00183 AC: 278AN: 152208Hom.: 3 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
278
AN:
152208
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000538 AC: 135AN: 250708Hom.: 1 AF XY: 0.000362 AC XY: 49AN XY: 135534
GnomAD3 exomes
AF:
AC:
135
AN:
250708
Hom.:
AF XY:
AC XY:
49
AN XY:
135534
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000208 AC: 304AN: 1461164Hom.: 1 Cov.: 31 AF XY: 0.000160 AC XY: 116AN XY: 726826
GnomAD4 exome
AF:
AC:
304
AN:
1461164
Hom.:
Cov.:
31
AF XY:
AC XY:
116
AN XY:
726826
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00183 AC: 278AN: 152326Hom.: 3 Cov.: 33 AF XY: 0.00180 AC XY: 134AN XY: 74486
GnomAD4 genome
?
AF:
AC:
278
AN:
152326
Hom.:
Cov.:
33
AF XY:
AC XY:
134
AN XY:
74486
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ESP6500AA
AF:
AC:
30
ESP6500EA
AF:
AC:
0
ExAC
?
AF:
AC:
73
Asia WGS
AF:
AC:
2
AN:
3478
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 submitter | clinical testing | Invitae | Sep 11, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M
MutationTaster
Benign
D;D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;.;N
REVEL
Benign
Sift
Benign
D;.;D
Sift4G
Benign
T;T;T
Polyphen
D;D;D
Vest4
MutPred
Loss of stability (P = 0.1827);Loss of stability (P = 0.1827);Loss of stability (P = 0.1827);
MVP
MPC
0.37
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at