Genetic Variant ENST00000561649.4:n.428A>G (chr16-1299208-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000561649.4(ENSG00000260710):n.428A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,016 control chromosomes in the GnomAD database, including 36,730 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 0.69 ( 36709 hom., cov: 32)

Exomes 𝑓: 0.76 ( 21 hom. )

Consequence

ENSG00000260710
ENST00000561649.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.770

Publications

26 publications found

Variant links:

Genes affected

ENSG00000260710 (HGNC:58131):

ENSG00000260710 links:

UBE2I (HGNC:12485): (ubiquitin conjugating enzyme E2 I) The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ligases, or E3s. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. Four alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

UBE2I links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
UBE2I-AS1	NR_198995.1 link	n.398A>G	non_coding_transcript_exon_variant	Exon 1 of 3
UBE2I-AS1	NR_198996.1 link	n.398A>G	non_coding_transcript_exon_variant	Exon 1 of 2
UBE2I-AS1	NR_198997.1 link	n.398A>G	non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000260710	ENST00000561649.4 link	n.428A>G	non_coding_transcript_exon_variant	Exon 1 of 3	3
ENSG00000260710	ENST00000686290.3 link	n.362A>G	non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000260710	ENST00000690088.3 link	n.428A>G	non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.691

AC:

104917

AN:

151826

Hom.:

36697

Cov.:

show subpopulations

Gnomad AFR

AF:

0.599

Gnomad AMI

AF:

0.750

Gnomad AMR

AF:

0.648

Gnomad ASJ

AF:

0.722

Gnomad EAS

AF:

0.911

Gnomad SAS

AF:

0.776

Gnomad FIN

AF:

0.769

Gnomad MID

AF:

0.671

Gnomad NFE

AF:

0.720

Gnomad OTH

AF:

0.672

GnomAD4 exome

AF:

0.764

AC:

AN:

Hom.:

Cov.:

AF XY:

0.725

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.833

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.696

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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

AF:

0.691

AC:

104976

AN:

151944

Hom.:

36709

Cov.:

AF XY:

0.695

AC XY:

51634

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.599

AC:

24776

AN:

41374

American (AMR)

AF:

0.647

AC:

9871

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.722

AC:

2505

AN:

3470

East Asian (EAS)

AF:

0.911

AC:

4712

AN:

5172

South Asian (SAS)

AF:

0.776

AC:

3738

AN:

4820

European-Finnish (FIN)

AF:

0.769

AC:

8128

AN:

10564

Middle Eastern (MID)

AF:

0.656

AC:

193

AN:

294

European-Non Finnish (NFE)

AF:

0.720

AC:

48950

AN:

67976

Other (OTH)

AF:

0.674

AC:

1419

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1620

3240

4861

6481

8101

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

828

1656

2484

3312

4140

<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:

0.711

Hom.:

106691

Bravo

AF:

0.675

Asia WGS

AF:

0.833

AC:

2898

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

2.5

(source)

DANN

Benign

0.35

PhyloP100

-0.77

Mutation Taster

=100/0

polymorphism

(source)

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over