chr1-26293158-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001389556.1(UBXN11):​c.559+1047G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,082 control chromosomes in the GnomAD database, including 9,758 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.34 ( 9758 hom., cov: 32)

Consequence

UBXN11
NM_001389556.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.47
Variant links:
Genes affected
UBXN11 (HGNC:30600): (UBX domain protein 11) This gene encodes a protein with a divergent C-terminal UBX domain. The homologous protein in the rat interacts with members of the Rnd subfamily of Rho GTPases at the cell periphery through its C-terminal region. It also interacts with several heterotrimeric G proteins through their G-alpha subunits and promotes Rho GTPase activation. It is proposed to serve a bidirectional role in the promotion and inhibition of Rho activity through upstream signaling pathways. The 3' coding sequence of this gene contains a polymoprhic region of 24 nt tandem repeats. Several transcripts containing between 1.5 and five repeat units have been reported. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
UBXN11NM_001389556.1 linkuse as main transcriptc.559+1047G>A intron_variant ENST00000374222.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
UBXN11ENST00000374222.6 linkuse as main transcriptc.559+1047G>A intron_variant 5 NM_001389556.1 A2Q5T124-1

Frequencies

GnomAD3 genomes
AF:
0.343
AC:
52175
AN:
151964
Hom.:
9738
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.491
Gnomad AMI
AF:
0.258
Gnomad AMR
AF:
0.307
Gnomad ASJ
AF:
0.323
Gnomad EAS
AF:
0.151
Gnomad SAS
AF:
0.306
Gnomad FIN
AF:
0.318
Gnomad MID
AF:
0.326
Gnomad NFE
AF:
0.286
Gnomad OTH
AF:
0.326
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.343
AC:
52237
AN:
152082
Hom.:
9758
Cov.:
32
AF XY:
0.345
AC XY:
25651
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.491
Gnomad4 AMR
AF:
0.306
Gnomad4 ASJ
AF:
0.323
Gnomad4 EAS
AF:
0.152
Gnomad4 SAS
AF:
0.308
Gnomad4 FIN
AF:
0.318
Gnomad4 NFE
AF:
0.286
Gnomad4 OTH
AF:
0.321
Alfa
AF:
0.294
Hom.:
9602
Bravo
AF:
0.346
Asia WGS
AF:
0.236
AC:
820
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.71
DANN
Benign
0.68

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: rs6598955; hg19: chr1-26619649; COSMIC: COSV59025087; COSMIC: COSV59025087; API