rs6598955

Positions:

• chr1-26293158-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

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
UBXN11	NM_001389556.1	c.559+1047G>A		intron_variant		ENST00000374222.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBXN11	ENST00000374222.6	c.559+1047G>A		intron_variant		5	NM_001389556.1	A2

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

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

Other links and lift over

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