NM_024551.3:c.-86-6471T>G

Variant names:

• chr12-1747787-T-G
• rs12230440
• NM_024551.3:c.-86-6471T>G

Variant summary

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

The NM_024551.3(ADIPOR2):​c.-86-6471T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,152 control chromosomes in the GnomAD database, including 2,232 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 0.15 (2232 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 15 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.303 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	NM_024551.3	MANE Select	c.-86-6471T>G		intron	N/A	NP_078827.2
	ADIPOR2	NM_001375363.1		c.-86-6471T>G		intron	N/A	NP_001362292.1
	ADIPOR2	NM_001375364.1		c.-86-6471T>G		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.-86-6471T>G		intron	N/A	ENSP00000349616.4
	ADIPOR2	ENST00000537545.1	TSL:3	n.145-6471T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22065 AN: 152034 Hom.: 2227 Cov.: 32

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.145 AC: 22088 AN: 152152 Hom.: 2232 Cov.: 32 AF XY: 0.147 AC XY: 10971 AN XY: 74388

African (AFR) AF: 0.0435 AC: 1806 AN: 41552

American (AMR) AF: 0.310 AC: 4739 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 567 AN: 3470

East Asian (EAS) AF: 0.277 AC: 1431 AN: 5164

South Asian (SAS) AF: 0.213 AC: 1026 AN: 4822

European-Finnish (FIN) AF: 0.106 AC: 1116 AN: 10566

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10756 AN: 67990

Other (OTH) AF: 0.175 AC: 369 AN: 2106

Alfa AF: 0.161 Hom.: 5332

Bravo AF: 0.159

Asia WGS AF: 0.221 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	10
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: rs12230440; hg19: chr12-1856953;