rs929434

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024551.3(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_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADIPOR2	NM_024551.3	c.-86-1335G>A		intron_variant		ENST00000357103.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.-86-1335G>A		intron_variant		1	NM_024551.3	P1
ADIPOR2	ENST00000537545.1	n.145-1335G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.357

Alfa AF: 0.298 Hom.: 3785

Bravo AF: 0.320

Asia WGS AF: 0.433 AC: 1502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.39

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

Publications

LitVar

Other links and lift over

dbSNP: rs929434; hg19: chr12-1862089;