12-1782206-C-T

Variant names:

• chr12-1782206-C-T
• rs2286383
• NM_024551.3:c.838+1130C>T

Variant summary

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

The NM_024551.3(ADIPOR2):​c.838+1130C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 152,052 control chromosomes in the GnomAD database, including 22,749 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 0.54 (22749 hom., cov: 33)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• Publications: 11 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 (AFR) allele frequency at 95% confidence interval = 0.668 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.838+1130C>T		intron	N/A	NP_078827.2
	ADIPOR2	NM_001375363.1		c.839-806C>T		intron	N/A	NP_001362292.1
	ADIPOR2	NM_001375364.1		c.838+1130C>T		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.838+1130C>T		intron	N/A	ENSP00000349616.4	Q86V24
	ADIPOR2	ENST00000878990.1		c.917-800C>T		intron	N/A	ENSP00000549049.1
	ADIPOR2	ENST00000878964.1		c.839-800C>T		intron	N/A	ENSP00000549023.1

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81675 AN: 151932 Hom.: 22709 Cov.: 33

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.538 AC: 81769 AN: 152052 Hom.: 22749 Cov.: 33 AF XY: 0.541 AC XY: 40228 AN XY: 74318

African (AFR) AF: 0.674 AC: 27962 AN: 41464

American (AMR) AF: 0.609 AC: 9311 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1668 AN: 3468

East Asian (EAS) AF: 0.597 AC: 3088 AN: 5174

South Asian (SAS) AF: 0.556 AC: 2676 AN: 4814

European-Finnish (FIN) AF: 0.471 AC: 4976 AN: 10566

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30387 AN: 67962

Other (OTH) AF: 0.564 AC: 1193 AN: 2114

Alfa AF: 0.471 Hom.: 8878

Bravo AF: 0.556

Asia WGS AF: 0.595 AC: 2066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.4
DANN	Benign	0.26
PhyloP100		-0.35
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: rs2286383; hg19: chr12-1891372;