chr11-5517909-G-A

Position:

• chr11-5517909-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000380259.7(ENSG00000239920):​n.*739+72916C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,142 control chromosomes in the GnomAD database, including 6,516 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 (6516 hom., cov: 33)
• Consequence: ENSG00000239920 ENST00000380259.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.5517909G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000239920	ENST00000380259.7	n.*739+72916C>T		intron_variant		5		ENSP00000369609.3
UBQLNL	ENST00000673910.1	c.-2+401C>T		intron_variant				ENSP00000501246.1

Frequencies

GnomAD3 genomes AF: 0.289 AC: 44006 AN: 152024 Hom.: 6507 Cov.: 33

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.289 AC: 44045 AN: 152142 Hom.: 6516 Cov.: 33 AF XY: 0.285 AC XY: 21232 AN XY: 74372

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.292

Alfa AF: 0.312 Hom.: 15328

Bravo AF: 0.291

Asia WGS AF: 0.252 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.23
DANN	Benign	0.72

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: rs979752; hg19: chr11-5539139;