11-5514299-G-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBQLNL	NM_145053.5	c.*715C>A		downstream_gene_variant		ENST00000380184.2	NP_659490.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000239920	ENST00000380259.7	n.*739+76526C>A		intron_variant	Intron 5 of 7	5		ENSP00000369609.3
UBQLNL	ENST00000380184.2	c.*715C>A		downstream_gene_variant		6	NM_145053.5	ENSP00000369531.1
UBQLNL	ENST00000673910.1	c.*715C>A		downstream_gene_variant				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

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.278

Alfa AF: 0.263 Hom.: 9206

Bravo AF: 0.281

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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: rs10838245; hg19: chr11-5535529;