rs467465

Variant names:

• chr15-84421670-T-C
• rs467465
• ENST00000734072.1:n.701A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000734072.1(ENSG00000290690):​n.701A>G variant causes a non coding transcript exon 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: ENSG00000290690 ENST00000734072.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 1 publications found

Genes affected

ENSG00000290690 (HGNC:):

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

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
ENSG00000290690	ENST00000734072.1	n.701A>G		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000259774	ENST00000734452.1	n.66T>C		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000259774	ENST00000734453.1	n.129T>C		non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.00811 AC: 850 AN: 104794 Hom.: 2 Cov.: 16

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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0682 AC: 3 AN: 44

American (AMR) AF: 0.00519 AC: 3 AN: 578

Ashkenazi Jewish (ASJ) AF: 0.0549 AC: 9 AN: 164

East Asian (EAS) AF: 0.00 AC: 0 AN: 54

South Asian (SAS) AF: 0.158 AC: 560 AN: 3540

European-Finnish (FIN) AF: 0.0544 AC: 47 AN: 864

Middle Eastern (MID) AF: 0.0526 AC: 2 AN: 38

European-Non Finnish (NFE) AF: 0.0389 AC: 319 AN: 8204

Other (OTH) AF: 0.0387 AC: 24 AN: 620

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00552 AC: 167 AN: 30256

American (AMR) AF: 0.00426 AC: 46 AN: 10790

Ashkenazi Jewish (ASJ) AF: 0.00952 AC: 22 AN: 2312

East Asian (EAS) AF: 0.00196 AC: 8 AN: 4088

South Asian (SAS) AF: 0.00879 AC: 30 AN: 3414

European-Finnish (FIN) AF: 0.00829 AC: 55 AN: 6638

Middle Eastern (MID) AF: 0.0108 AC: 2 AN: 186

European-Non Finnish (NFE) AF: 0.0109 AC: 497 AN: 45404

Other (OTH) AF: 0.0119 AC: 17 AN: 1428

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs467465; hg19: chr15-84976368;