rs979752

Variant names:

• chr11-5517909-G-A
• rs979752
• ENST00000380259.7:n.*739+72916C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-5517909-G-A
• chr11-5517909-G-C

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000239920	ENST00000380259.7	n.*739+72916C>T		intron_variant	Intron 5 of 7	5		ENSP00000369609.3
UBQLNL	ENST00000673910.1	c.-2+401C>T		intron_variant	Intron 1 of 1			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;