Genetic Variant ENST00000734072.1:n.701A>G (chr15-84421670-T-C) – ACMG Classification: Likely_benign (-4 pts)

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00400

Publications

1 publications found

Variant links:

Genes affected

ENSG00000290690 (HGNC:):

ENSG00000290690 links:

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

UBE2Q2P11 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000734072.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
ENSG00000290690	ENST00000734072.1	n.701A>G	non_coding_transcript_exon	Exon 1 of 2
ENSG00000259774	ENST00000734452.1	n.66T>C	non_coding_transcript_exon	Exon 1 of 4
ENSG00000259774	ENST00000734453.1	n.129T>C	non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.00811

AC:

850

AN:

104794

Hom.:

Cov.:

show subpopulations

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.:

AF XY:

0.0818

AC XY:

681

AN XY:

8322

show subpopulations

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

African (AFR)

AF:

0.0682

AC:

AN:

American (AMR)

AF:

0.00519

AC:

AN:

578

Ashkenazi Jewish (ASJ)

AF:

0.0549

AC:

AN:

164

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.158

AC:

560

AN:

3540

European-Finnish (FIN)

AF:

0.0544

AC:

AN:

864

Middle Eastern (MID)

AF:

0.0526

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0389

AC:

319

AN:

8204

Other (OTH)

AF:

0.0387

AC:

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.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.308

Heterozygous variant carriers

150

226

301

376

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00810

AC:

850

AN:

104908

Hom.:

Cov.:

AF XY:

0.00886

AC XY:

452

AN XY:

51008

show subpopulations

⚠️ 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:

AN:

10790

Ashkenazi Jewish (ASJ)

AF:

0.00952

AC:

AN:

2312

East Asian (EAS)

AF:

0.00196

AC:

AN:

4088

South Asian (SAS)

AF:

0.00879

AC:

AN:

3414

European-Finnish (FIN)

AF:

0.00829

AC:

AN:

6638

Middle Eastern (MID)

AF:

0.0108

AC:

AN:

186

European-Non Finnish (NFE)

AF:

0.0109

AC:

497

AN:

45404

Other (OTH)

AF:

0.0119

AC:

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.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.271

Heterozygous variant carriers

194

292

389

486

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.118

Hom.:

131

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

(source)

DANN

Benign

0.14

PhyloP100

-0.0040

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over