11-74005232-G-A

Variant names:

• chr11-74005232-G-A
• rs2734827
• NM_003356.4:c.541+498C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003356.4(UCP3):​c.541+498C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,004 control chromosomes in the GnomAD database, including 12,389 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 0.39 (12389 hom., cov: 32)
• Consequence: UCP3 NM_003356.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528
• Publications: 24 publications found

Genes affected

UCP3 (HGNC:12519): (uncoupling protein 3) 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. The different UCPs have tissue-specific expression; this gene is primarily expressed in skeletal muscle. This gene's protein product is postulated to protect mitochondria against lipid-induced oxidative stress. Expression levels of this gene increase when fatty acid supplies to mitochondria exceed their oxidation capacity and the protein enables the export of fatty acids from mitochondria. UCPs contain the three solcar protein domains typically found in MACPs. Two splice variants have been found for this gene.[provided by RefSeq, Nov 2008]

ENSG00000298570 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003356.4. 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
	UCP3	NM_003356.4	MANE Select	c.541+498C>T		intron	N/A	NP_003347.1
	UCP3	NM_022803.3		c.541+498C>T		intron	N/A	NP_073714.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UCP3	ENST00000314032.9	TSL:1 MANE Select	c.541+498C>T		intron	N/A	ENSP00000323740.4
	UCP3	ENST00000426995.2	TSL:1	c.541+498C>T		intron	N/A	ENSP00000392143.2
	ENSG00000298570	ENST00000756620.1		n.419+215G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59582 AN: 151888 Hom.: 12377 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.392 AC: 59644 AN: 152004 Hom.: 12389 Cov.: 32 AF XY: 0.386 AC XY: 28701 AN XY: 74314

African (AFR) AF: 0.532 AC: 22039 AN: 41436

American (AMR) AF: 0.403 AC: 6149 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1329 AN: 3468

East Asian (EAS) AF: 0.170 AC: 882 AN: 5174

South Asian (SAS) AF: 0.290 AC: 1399 AN: 4824

European-Finnish (FIN) AF: 0.272 AC: 2876 AN: 10570

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.349 AC: 23715 AN: 67952

Other (OTH) AF: 0.384 AC: 810 AN: 2110

Alfa AF: 0.361 Hom.: 18679

Bravo AF: 0.409

Asia WGS AF: 0.224 AC: 780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.67
PhyloP100		-0.53
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2734827; hg19: chr11-73716277;