NM_024551.3:c.-86-6442T>C

Variant names:

• chr12-1747816-T-C
• rs10773989
• NM_024551.3:c.-86-6442T>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.-86-6442T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,914 control chromosomes in the GnomAD database, including 13,918 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 0.42 (13918 hom., cov: 31)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 12 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 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.-86-6442T>C		intron	N/A	NP_078827.2
	ADIPOR2	NM_001375363.1		c.-86-6442T>C		intron	N/A	NP_001362292.1
	ADIPOR2	NM_001375364.1		c.-86-6442T>C		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.-86-6442T>C		intron	N/A	ENSP00000349616.4	Q86V24
	ADIPOR2	ENST00000878990.1		c.-86-6442T>C		intron	N/A	ENSP00000549049.1
	ADIPOR2	ENST00000878964.1		c.-86-6442T>C		intron	N/A	ENSP00000549023.1

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63219 AN: 151796 Hom.: 13909 Cov.: 31

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.416 AC: 63253 AN: 151914 Hom.: 13918 Cov.: 31 AF XY: 0.413 AC XY: 30702 AN XY: 74252

African (AFR) AF: 0.276 AC: 11437 AN: 41432

American (AMR) AF: 0.370 AC: 5652 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1587 AN: 3466

East Asian (EAS) AF: 0.474 AC: 2448 AN: 5164

South Asian (SAS) AF: 0.428 AC: 2065 AN: 4822

European-Finnish (FIN) AF: 0.448 AC: 4709 AN: 10502

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33903 AN: 67952

Other (OTH) AF: 0.389 AC: 818 AN: 2102

Alfa AF: 0.456 Hom.: 6237

Bravo AF: 0.402

Asia WGS AF: 0.437 AC: 1523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	12
DANN	Benign	0.53
PhyloP100		0.21
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: rs10773989; hg19: chr12-1856982;