rs767870

Variant names:

• chr12-1780657-G-A
• rs767870
• NM_024551.3:c.650+20G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 30 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024551.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	NM_024551.3	MANE Select	c.650+20G>A		intron	N/A	NP_078827.2
	ADIPOR2	NM_001375363.1		c.650+20G>A		intron	N/A	NP_001362292.1
	ADIPOR2	NM_001375364.1		c.650+20G>A		intron	N/A	NP_001362293.1	Q86V24

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	ENST00000357103.5	TSL:1 MANE Select	c.650+20G>A		intron	N/A	ENSP00000349616.4	Q86V24
	ADIPOR2	ENST00000878990.1		c.728+20G>A		intron	N/A	ENSP00000549049.1
	ADIPOR2	ENST00000878964.1		c.650+20G>A		intron	N/A	ENSP00000549023.1

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

GnomAD2 exomes AF: 0.825 AC: 158636 AN: 192308 AF XY: 0.833

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 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

African (AFR) AF: 0.375 AC: 11009 AN: 29382

American (AMR) AF: 0.897 AC: 25480 AN: 28412

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 18716 AN: 22578

East Asian (EAS) AF: 0.926 AC: 34662 AN: 37416

South Asian (SAS) AF: 0.830 AC: 61456 AN: 74046

European-Finnish (FIN) AF: 0.881 AC: 44534 AN: 50532

Middle Eastern (MID) AF: 0.821 AC: 4205 AN: 5124

European-Non Finnish (NFE) AF: 0.849 AC: 914085 AN: 1076794

Other (OTH) AF: 0.822 AC: 46658 AN: 56732

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

African (AFR) AF: 0.394 AC: 16318 AN: 41390

American (AMR) AF: 0.849 AC: 12969 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2866 AN: 3468

East Asian (EAS) AF: 0.895 AC: 4634 AN: 5176

South Asian (SAS) AF: 0.819 AC: 3935 AN: 4806

European-Finnish (FIN) AF: 0.889 AC: 9408 AN: 10582

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.843 AC: 57334 AN: 67998

Other (OTH) AF: 0.750 AC: 1583 AN: 2110

Alfa AF: 0.779 Hom.: 23459

Bravo AF: 0.710

Asia WGS AF: 0.816 AC: 2836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0010
DANN	Benign	0.44
PhyloP100		-1.6
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: rs767870; hg19: chr12-1889823;