11-5514299-G-T

Variant names:

• chr11-5514299-G-T
• rs10838245
• ENST00000380259.7:n.*739+76526C>A

Variant summary

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

The ENST00000380259.7(ENSG00000239920):​n.*739+76526C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,664 control chromosomes in the GnomAD database, including 6,833 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 0.29 (6833 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000239920 ENST00000380259.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30
• Publications: 7 publications found

Genes affected

ENSG00000239920 (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000380259.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBQLNL	NM_145053.5	MANE Select	c.*715C>A		downstream_gene	N/A	NP_659490.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000239920	ENST00000380259.7	TSL:5	n.*739+76526C>A		intron	N/A	ENSP00000369609.3
	UBQLNL	ENST00000380184.2	TSL:6 MANE Select	c.*715C>A		downstream_gene	N/A	ENSP00000369531.1
	UBQLNL	ENST00000673910.1		c.*715C>A		downstream_gene	N/A	ENSP00000501246.1

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44438 AN: 151574 Hom.: 6822 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.279

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.293 AC: 44489 AN: 151664 Hom.: 6833 Cov.: 32 AF XY: 0.300 AC XY: 22218 AN XY: 74120

African (AFR) AF: 0.282 AC: 11654 AN: 41354

American (AMR) AF: 0.317 AC: 4830 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 702 AN: 3470

East Asian (EAS) AF: 0.391 AC: 2013 AN: 5154

South Asian (SAS) AF: 0.286 AC: 1375 AN: 4802

European-Finnish (FIN) AF: 0.424 AC: 4429 AN: 10438

Middle Eastern (MID) AF: 0.292 AC: 84 AN: 288

European-Non Finnish (NFE) AF: 0.274 AC: 18604 AN: 67904

Other (OTH) AF: 0.278 AC: 581 AN: 2088

Alfa AF: 0.271 Hom.: 21995

Bravo AF: 0.281

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.19
DANN	Benign	0.48
PhyloP100		-1.3
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

Other links and lift over

dbSNP: rs10838245; hg19: chr11-5535529;