rs10773982

Variant names:

• chr12-1718983-G-A
• rs10773982
• NM_024551.3:c.-87+27792G>A

Variant summary

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

The NM_001375363.1(ADIPOR2):​c.-87+27792G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,036 control chromosomes in the GnomAD database, including 30,258 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 0.63 (30258 hom., cov: 32)
• Consequence: ADIPOR2 NM_001375363.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 13 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375363.1. 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
	ADIPOR2	NM_024551.3	MANE Select	c.-87+27792G>A		intron	N/A	NP_078827.2
	ADIPOR2	NM_001375363.1		c.-87+27792G>A		intron	N/A	NP_001362292.1
	ADIPOR2	NM_001375364.1		c.-248-17096G>A		intron	N/A	NP_001362293.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	ENST00000357103.5	TSL:1 MANE Select	c.-87+27792G>A		intron	N/A	ENSP00000349616.4
	ADIPOR2	ENST00000878990.1		c.-87+27792G>A		intron	N/A	ENSP00000549049.1
	ADIPOR2	ENST00000878964.1		c.-87+27792G>A		intron	N/A	ENSP00000549023.1

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95417 AN: 151918 Hom.: 30240 Cov.: 32

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.628 AC: 95478 AN: 152036 Hom.: 30258 Cov.: 32 AF XY: 0.623 AC XY: 46318 AN XY: 74308

African (AFR) AF: 0.633 AC: 26253 AN: 41458

American (AMR) AF: 0.498 AC: 7609 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2260 AN: 3466

East Asian (EAS) AF: 0.501 AC: 2594 AN: 5174

South Asian (SAS) AF: 0.605 AC: 2915 AN: 4820

European-Finnish (FIN) AF: 0.619 AC: 6528 AN: 10554

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45298 AN: 67980

Other (OTH) AF: 0.600 AC: 1267 AN: 2112

Alfa AF: 0.641 Hom.: 37370

Bravo AF: 0.615

Asia WGS AF: 0.542 AC: 1886 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.77
DANN	Benign	0.62
PhyloP100		0.0
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: rs10773982; hg19: chr12-1828149;