ENST00000660751.1:n.261C>T

Variant names:

Variant summary

Our verdict is . The variant received -12 classification points (ACMG Germline Pathogenicity v2019): 0P and 12B. BA1BP4_Strong

The ENST00000660751.1(ENSG00000287425):n.261C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a cumulative frequency of 0.4 (AC=60,914) in the gnomAD database across 152,158 control chromosomes, including 12,224 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.448. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. Variant has been reported in ClinVar as Uncertain Significance (no review stars).

Frequency

Genomes: 𝑓 0.40 ( 12224 hom., cov: 33)

Consequence

ENSG00000287425
ENST00000660751.1 non_coding_transcript_exon

Scores

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: -0.0280

Publications

305 publications found

Variant links:

Genes affected

ENSG00000287425 (HGNC:):

ENSG00000287425 links:

UCP2 (HGNC:12518): (uncoupling protein 2) Mitochondrial uncoupling proteins (UCP) are members of the larger family of mitochondrial anion carrier proteins (MACP). UCPs separate oxidative phosphorylation from ATP synthesis with energy dissipated as heat, also referred to as the mitochondrial proton leak. UCPs facilitate the transfer of anions from the inner to the outer mitochondrial membrane and the return transfer of protons from the outer to the inner mitochondrial membrane. They also reduce the mitochondrial membrane potential in mammalian cells. Tissue specificity occurs for the different UCPs and the exact methods of how UCPs transfer H+/OH- are not known. UCPs contain the three homologous protein domains of MACPs. This gene is expressed in many tissues, with the greatest expression in skeletal muscle. It is thought to play a role in nonshivering thermogenesis, obesity and diabetes. Chromosomal order is 5'-UCP3-UCP2-3'. [provided by RefSeq, Jul 2008]

UCP2 Gene-Disease associations (from GenCC):

hyperinsulinism due to UCP2 deficiency
Inheritance: AD Classification: MODERATE, SUPPORTIVE Submitted by: PanelApp Australia, Orphanet

UCP2 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000660751.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript

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

BP4

Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).

BA1

GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.4476 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: ENST00000660751.1. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287425	ENST00000660751.1		n.261C>T		non_coding_transcript_exon	Exon 1 of 1
	UCP2	ENST00000952750.1		c.-682G>A		upstream_gene	N/A	ENSP00000622809.1

Frequencies

GnomAD3 genomes

AF:

0.401

AC:

60896

AN:

152040

Hom.:

12223

Cov.:

show subpopulations

Gnomad AFR

AF:

0.454

Gnomad AMI

AF:

0.253

Gnomad AMR

AF:

0.427

Gnomad ASJ

AF:

0.308

Gnomad EAS

AF:

0.426

Gnomad SAS

AF:

0.348

Gnomad FIN

AF:

0.398

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.376

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.400

AC:

60914

AN:

152158

Hom.:

12224

Cov.:

AF XY:

0.401

AC XY:

29808

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.453

AC:

18805

AN:

41508

American (AMR)

AF:

0.428

AC:

6536

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.308

AC:

1071

AN:

3472

East Asian (EAS)

AF:

0.426

AC:

2205

AN:

5172

South Asian (SAS)

AF:

0.346

AC:

1666

AN:

4820

European-Finnish (FIN)

AF:

0.398

AC:

4219

AN:

10588

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.372

AC:

25303

AN:

67998

Other (OTH)

AF:

0.372

AC:

786

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1958

3916

5874

7832

9790

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

576

1152

1728

2304

2880

<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:

0.379

Hom.:

48775

Bravo

AF:

0.406

Asia WGS

AF:

0.387

AC:

1343

AN:

3478

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.492

AC:

60387

AN:

122728

Turkish Variome

AF:

0.336

AC:

520

AN:

1546

Hom.:

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.408

AC:

3657

AN:

8960

Hom.:

774

ABraOM SABE-WGS-1171

AF:

0.398

AC:

933

AN:

2342

Hom.:

194

ClinVar

ClinVar submissions

Significance:risk factor

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

BODY MASS INDEX QUANTITATIVE TRAIT LOCUS 4 (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

4.3

(source)

DANN

Benign

0.74

PhyloP100

-0.028

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Local populations

ClinVar

Computational scores

Splicing

Publications

Other links and lift over