rs4766413

Variant names:

• chr12-1724622-G-A
• rs4766413
• NM_024551.3:c.-86-29636G>A

Variant summary

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

The NM_024551.3(ADIPOR2):​c.-86-29636G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,050 control chromosomes in the GnomAD database, including 36,685 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 0.69 (36685 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 5 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.-86-29636G>A		intron_variant	Intron 1 of 7	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.-86-29636G>A		intron_variant	Intron 1 of 7	1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	n.145-29636G>A		intron_variant	Intron 1 of 2	3
ADIPOR2	ENST00000540974.1	n.149-6103G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105046 AN: 151934 Hom.: 36648 Cov.: 32

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.691 AC: 105136 AN: 152050 Hom.: 36685 Cov.: 32 AF XY: 0.690 AC XY: 51315 AN XY: 74328

African (AFR) AF: 0.708 AC: 29346 AN: 41462

American (AMR) AF: 0.544 AC: 8324 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2392 AN: 3470

East Asian (EAS) AF: 0.677 AC: 3500 AN: 5168

South Asian (SAS) AF: 0.653 AC: 3141 AN: 4810

European-Finnish (FIN) AF: 0.752 AC: 7944 AN: 10564

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48327 AN: 67968

Other (OTH) AF: 0.661 AC: 1394 AN: 2110

Alfa AF: 0.702 Hom.: 22327

Bravo AF: 0.674

Asia WGS AF: 0.676 AC: 2354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.67
DANN	Benign	0.42
PhyloP100		-1.5
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: rs4766413; hg19: chr12-1833788;