12-1787790-C-T

Position:

• chr12-1787790-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024551.3(ADIPOR2):​c.*1718C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,128 control chromosomes in the GnomAD database, including 12,407 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 (12404 hom., cov: 32)
  • Exomes 𝑓: 0.40 (3 hom.)
• Consequence: ADIPOR2 NM_024551.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

Genes affected

ADIPOR2 (HGNC:24041): (adiponectin receptor 2) The adiponectin receptors, ADIPOR1 (MIM 607945) and ADIPOR2, serve as receptors for globular and full-length adiponectin (MIM 605441) and mediate increased AMPK (see MIM 602739) and PPAR-alpha (PPARA; MIM 170998) ligand activities, as well as fatty acid oxidation and glucose uptake by adiponectin (Yamauchi et al., 2003 [PubMed 12802337]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.*1718C>T		3_prime_UTR_variant	8/8	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.*1718C>T		3_prime_UTR_variant	8/8	1	NM_024551.3	ENSP00000349616.4

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58853 AN: 151980 Hom.: 12402 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.384

GnomAD4 exome AF: 0.400 AC: 12 AN: 30 Hom.: 3 Cov.: 0 AF XY: 0.500 AC XY: 8 AN XY: 16

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 FIN exome AF: 0.563

Gnomad4 NFE exome AF: 0.333

GnomAD4 genome AF: 0.387 AC: 58869 AN: 152098 Hom.: 12404 Cov.: 32 AF XY: 0.386 AC XY: 28724 AN XY: 74332

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.386

Alfa AF: 0.457 Hom.: 22482

Bravo AF: 0.370

Asia WGS AF: 0.378 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.46

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

Publications

LitVar

Other links and lift over

dbSNP: rs1044471; hg19: chr12-1896956;