rs1468491

Variant names:

• chr12-1762988-G-C
• rs1468491
• NM_024551.3:c.171+8474G>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.171+8474G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,158 control chromosomes in the GnomAD database, including 1,520 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 0.13 (1520 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.554
• Publications: 1 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=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.171+8474G>C		intron_variant	Intron 2 of 7	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.171+8474G>C		intron_variant	Intron 2 of 7	1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	n.401+8474G>C		intron_variant	Intron 2 of 2	3
ADIPOR2	ENST00000543456.1	n.252+2008G>C		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20319 AN: 152040 Hom.: 1520 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.0907

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.0740

Gnomad FIN AF: 0.0990

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.134 AC: 20329 AN: 152158 Hom.: 1520 Cov.: 32 AF XY: 0.130 AC XY: 9681 AN XY: 74368

African (AFR) AF: 0.195 AC: 8096 AN: 41486

American (AMR) AF: 0.0842 AC: 1288 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0907 AC: 315 AN: 3472

East Asian (EAS) AF: 0.0243 AC: 126 AN: 5186

South Asian (SAS) AF: 0.0745 AC: 359 AN: 4818

European-Finnish (FIN) AF: 0.0990 AC: 1048 AN: 10586

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.129 AC: 8778 AN: 68006

Other (OTH) AF: 0.127 AC: 268 AN: 2106

Alfa AF: 0.137 Hom.: 195

Bravo AF: 0.136

Asia WGS AF: 0.0520 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	10
DANN	Benign	0.92
PhyloP100		0.55
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: rs1468491; hg19: chr12-1872154;