rs929434

Variant names:

• chr12-1752923-G-A
• rs929434
• NM_024551.3:c.-86-1335G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-1752923-G-A
• chr12-1752923-G-T

Variant summary

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

The NM_001375363.1(ADIPOR2):​c.-86-1335G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,042 control chromosomes in the GnomAD database, including 8,174 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 0.31 (8174 hom., cov: 31)
• Consequence: ADIPOR2 NM_001375363.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375363.1. 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.-86-1335G>A		intron	N/A	NP_078827.2
	ADIPOR2	NM_001375363.1		c.-86-1335G>A		intron	N/A	NP_001362292.1
	ADIPOR2	NM_001375364.1		c.-86-1335G>A		intron	N/A	NP_001362293.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	ENST00000357103.5	TSL:1 MANE Select	c.-86-1335G>A		intron	N/A	ENSP00000349616.4
	ADIPOR2	ENST00000878990.1		c.-86-1335G>A		intron	N/A	ENSP00000549049.1
	ADIPOR2	ENST00000878964.1		c.-86-1335G>A		intron	N/A	ENSP00000549023.1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47487 AN: 151920 Hom.: 8168 Cov.: 31

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.313 AC: 47525 AN: 152042 Hom.: 8174 Cov.: 31 AF XY: 0.319 AC XY: 23742 AN XY: 74322

African (AFR) AF: 0.196 AC: 8139 AN: 41478

American (AMR) AF: 0.480 AC: 7332 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1219 AN: 3468

East Asian (EAS) AF: 0.492 AC: 2545 AN: 5170

South Asian (SAS) AF: 0.398 AC: 1923 AN: 4826

European-Finnish (FIN) AF: 0.369 AC: 3893 AN: 10556

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21283 AN: 67954

Other (OTH) AF: 0.357 AC: 751 AN: 2104

Alfa AF: 0.299 Hom.: 4217

Bravo AF: 0.320

Asia WGS AF: 0.433 AC: 1502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.39
PhyloP100		-0.14
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: rs929434; hg19: chr12-1862089;