rs767870

Positions:

• chr12-1780657-G-A
• chr12-1780657-G-C

Variant summary

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

The NM_024551.3(ADIPOR2):​c.650+20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 1,533,030 control chromosomes in the GnomAD database, including 535,024 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 0.72 (43204 hom., cov: 31)
  • Exomes 𝑓: 0.84 (491820 hom.)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.650+20G>A		intron_variant		ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.650+20G>A		intron_variant		1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537190.1	n.490+20G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110110 AN: 151896 Hom.: 43190 Cov.: 31

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.750

GnomAD3 exomes AF: 0.825 AC: 158636 AN: 192308 Hom.: 66944 AF XY: 0.833 AC XY: 87859 AN XY: 105468

Gnomad AFR exome AF: 0.387

Gnomad AMR exome AF: 0.905

Gnomad ASJ exome AF: 0.835

Gnomad EAS exome AF: 0.909

Gnomad SAS exome AF: 0.834

Gnomad FIN exome AF: 0.888

Gnomad NFE exome AF: 0.844

Gnomad OTH exome AF: 0.832

GnomAD4 exome AF: 0.841 AC: 1160805 AN: 1381016 Hom.: 491820 Cov.: 34 AF XY: 0.841 AC XY: 575529 AN XY: 684164

Gnomad4 AFR exome AF: 0.375

Gnomad4 AMR exome AF: 0.897

Gnomad4 ASJ exome AF: 0.829

Gnomad4 EAS exome AF: 0.926

Gnomad4 SAS exome AF: 0.830

Gnomad4 FIN exome AF: 0.881

Gnomad4 NFE exome AF: 0.849

Gnomad4 OTH exome AF: 0.822

GnomAD4 genome AF: 0.725 AC: 110167 AN: 152014 Hom.: 43204 Cov.: 31 AF XY: 0.731 AC XY: 54336 AN XY: 74312

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.849

Gnomad4 ASJ AF: 0.826

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.889

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.750

Alfa AF: 0.776 Hom.: 16467

Bravo AF: 0.710

Asia WGS AF: 0.816 AC: 2836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0010
DANN	Benign	0.44

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: rs767870; hg19: chr12-1889823;