rs467465

chr15-84421670-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000559691.1(UBE2Q2P11):n.102+66A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.0081 (2 hom., cov: 16)
  • Exomes 𝑓: 0.069 (3 hom.)
  • Failed GnomAD Quality Control
• Consequence: UBE2Q2P11 ENST00000559691.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

Genes affected

UBE2Q2P11 (HGNC:49522): (UBE2Q2 pseudogene 11)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBE2Q2P11	ENST00000559691.1	n.102+66A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 850 AN: 104794 Hom.: 2 Cov.: 16 FAILED QC

Gnomad AFR AF: 0.00554

Gnomad AMI AF: 0.0153

Gnomad AMR AF: 0.00427

Gnomad ASJ AF: 0.00952

Gnomad EAS AF: 0.00195

Gnomad SAS AF: 0.00879

Gnomad FIN AF: 0.00829

Gnomad MID AF: 0.0100

Gnomad NFE AF: 0.0109

Gnomad OTH AF: 0.0121

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0686 AC: 967 AN: 14106 Hom.: 3 AF XY: 0.0818 AC XY: 681 AN XY: 8322

Gnomad4 AFR exome AF: 0.0682

Gnomad4 AMR exome AF: 0.00519

Gnomad4 ASJ exome AF: 0.0549

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.158

Gnomad4 FIN exome AF: 0.0544

Gnomad4 NFE exome AF: 0.0389

Gnomad4 OTH exome AF: 0.0387

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00810 AC: 850 AN: 104908 Hom.: 2 Cov.: 16 AF XY: 0.00886 AC XY: 452 AN XY: 51008

Gnomad4 AFR AF: 0.00552

Gnomad4 AMR AF: 0.00426

Gnomad4 ASJ AF: 0.00952

Gnomad4 EAS AF: 0.00196

Gnomad4 SAS AF: 0.00879

Gnomad4 FIN AF: 0.00829

Gnomad4 NFE AF: 0.0109

Gnomad4 OTH AF: 0.0119

Alfa AF: 0.118 Hom.: 131

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	14
Dann	Benign	0.14

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs467465; hg19: chr15-84976368;