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GeneBe

11-5515529-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBS1BS2

The NM_145053.5(UBQLNL):c.913C>T(p.Gln305Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00221 in 1,614,108 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0079 ( 12 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 20 hom. )

Consequence

UBQLNL
NM_145053.5 stop_gained

Scores

1
6

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.254
Variant links:
Genes affected
UBQLNL (HGNC:28294): (ubiquilin like) Predicted to enable polyubiquitin modification-dependent protein binding activity. Predicted to be involved in ubiquitin-dependent protein catabolic process. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

PM4
?
    PM4 - Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants
Stoplost variant in NM_145053.5 Downstream stopcodon found after 561 codons.
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-5515529-G-A is Benign according to our data. Variant chr11-5515529-G-A is described in ClinVar as [Benign]. Clinvar id is 715487.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00795 (1210/152272) while in subpopulation AFR AF= 0.0238 (991/41556). AF 95% confidence interval is 0.0226. There are 12 homozygotes in gnomad4. There are 578 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
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 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
UBQLNLNM_145053.5 linkuse as main transcriptc.913C>T p.Gln305Ter stop_gained 1/1 ENST00000380184.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
UBQLNLENST00000380184.2 linkuse as main transcriptc.913C>T p.Gln305Ter stop_gained 1/1 NM_145053.5 A2Q8IYU4-1
UBQLNLENST00000673910.1 linkuse as main transcriptc.883C>T p.Gln295Ter stop_gained 2/2 P4

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00791
AC:
1203
AN:
152154
Hom.:
11
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0237
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00569
Gnomad ASJ
AF:
0.0179
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.000691
Gnomad OTH
AF:
0.0100
GnomAD3 exomes
AF:
0.00317
AC:
796
AN:
251054
Hom.:
5
AF XY:
0.00256
AC XY:
347
AN XY:
135652
show subpopulations
Gnomad AFR exome
AF:
0.0242
Gnomad AMR exome
AF:
0.00312
Gnomad ASJ exome
AF:
0.0179
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000776
Gnomad OTH exome
AF:
0.00376
GnomAD4 exome
AF:
0.00162
AC:
2364
AN:
1461836
Hom.:
20
Cov.:
92
AF XY:
0.00155
AC XY:
1125
AN XY:
727210
show subpopulations
Gnomad4 AFR exome
AF:
0.0258
Gnomad4 AMR exome
AF:
0.00369
Gnomad4 ASJ exome
AF:
0.0187
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000928
Gnomad4 FIN exome
AF:
0.000169
Gnomad4 NFE exome
AF:
0.000495
Gnomad4 OTH exome
AF:
0.00402
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00795
AC:
1210
AN:
152272
Hom.:
12
Cov.:
32
AF XY:
0.00776
AC XY:
578
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.0238
Gnomad4 AMR
AF:
0.00569
Gnomad4 ASJ
AF:
0.0179
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000691
Gnomad4 OTH
AF:
0.00992
Alfa
AF:
0.00273
Hom.:
4
Bravo
AF:
0.00930
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.000519
AC:
2
ESP6500AA
AF:
0.0216
AC:
95
ESP6500EA
AF:
0.00163
AC:
14
ExAC
?
    Exome Aggregation Consortium database
AF:
0.00336
AC:
408
Asia WGS
AF:
0.00289
AC:
10
AN:
3478
EpiCase
AF:
0.00109
EpiControl
AF:
0.00124

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 testingInvitaeSep 21, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Uncertain
-0.030
Cadd
Pathogenic
34
Dann
Benign
0.95
Eigen
Benign
-0.11
Eigen_PC
Benign
-0.50
FATHMM_MKL
Benign
0.045
N
MutationTaster
Benign
1.0
N;D
Vest4
0.050
GERP RS
-0.35

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: rs80343871; hg19: chr11-5536759; API