rs6598955

Variant names:

• chr1-26293158-C-T
• rs6598955
• NM_001389556.1:c.559+1047G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 21 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001389556.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBXN11	NM_001389556.1	MANE Select	c.559+1047G>A		intron	N/A	NP_001376485.1	Q5T124-1
	UBXN11	NM_183008.3		c.559+1047G>A		intron	N/A	NP_892120.2	Q5T124-1
	UBXN11	NM_001389559.1		c.460+1047G>A		intron	N/A	NP_001376488.1	Q5T124-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBXN11	ENST00000374222.6	TSL:5 MANE Select	c.559+1047G>A		intron	N/A	ENSP00000363339.1	Q5T124-1
	UBXN11	ENST00000374223.5	TSL:1	c.-171+3761G>A		intron	N/A	ENSP00000363340.1	X6R8M6
	UBXN11	ENST00000472155.5	TSL:1	n.643+1047G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52175 AN: 151964 Hom.: 9738 Cov.: 32

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

African (AFR) AF: 0.491 AC: 20373 AN: 41470

American (AMR) AF: 0.306 AC: 4676 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1123 AN: 3472

East Asian (EAS) AF: 0.152 AC: 783 AN: 5168

South Asian (SAS) AF: 0.308 AC: 1486 AN: 4826

European-Finnish (FIN) AF: 0.318 AC: 3358 AN: 10572

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19430 AN: 67986

Other (OTH) AF: 0.321 AC: 678 AN: 2110

Alfa AF: 0.308 Hom.: 18142

Bravo AF: 0.346

Asia WGS AF: 0.236 AC: 820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.71
DANN	Benign	0.68
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6598955;

hg19: chr1-26619649;

COSMIC: COSV59025087;

COSMIC: COSV59025087;