chr12-1769210-G-A

Variant names:

• chr12-1769210-G-A
• rs7138701
• NM_024551.3:c.172-3632G>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.172-3632G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0659 in 152,188 control chromosomes in the GnomAD database, including 867 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 0.066 (867 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.833
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.172-3632G>A		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.172-3632G>A		intron_variant	Intron 2 of 7	1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	n.402-3632G>A		intron_variant	Intron 2 of 2	3
ADIPOR2	ENST00000543456.1	n.253-3632G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0657 AC: 9996 AN: 152070 Hom.: 863 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0377

Gnomad ASJ AF: 0.0377

Gnomad EAS AF: 0.0795

Gnomad SAS AF: 0.0821

Gnomad FIN AF: 0.00283

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00509

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0659 AC: 10032 AN: 152188 Hom.: 867 Cov.: 32 AF XY: 0.0660 AC XY: 4914 AN XY: 74422

African (AFR) AF: 0.193 AC: 7994 AN: 41486

American (AMR) AF: 0.0376 AC: 575 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0377 AC: 131 AN: 3472

East Asian (EAS) AF: 0.0799 AC: 414 AN: 5182

South Asian (SAS) AF: 0.0820 AC: 396 AN: 4830

European-Finnish (FIN) AF: 0.00283 AC: 30 AN: 10592

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00509 AC: 346 AN: 68016

Other (OTH) AF: 0.0625 AC: 132 AN: 2112

Alfa AF: 0.0477 Hom.: 103

Bravo AF: 0.0722

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.51
PhyloP100		0.83
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: rs7138701; hg19: chr12-1878376;