12-1722080-A-G

Variant names:

• chr12-1722080-A-G
• rs10773983
• NM_024551.3:c.-87+30889A>G

Variant summary

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

The NM_024551.3(ADIPOR2):​c.-87+30889A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,110 control chromosomes in the GnomAD database, including 26,698 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 0.56 (26698 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515

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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.-87+30889A>G		intron_variant	Intron 1 of 7	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.-87+30889A>G		intron_variant	Intron 1 of 7	1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	n.145-32178A>G		intron_variant	Intron 1 of 2	3
ADIPOR2	ENST00000540974.1	n.149-8645A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85452 AN: 151992 Hom.: 26697 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.562 AC: 85470 AN: 152110 Hom.: 26698 Cov.: 32 AF XY: 0.567 AC XY: 42166 AN XY: 74340

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.685

Gnomad4 OTH AF: 0.553

Alfa AF: 0.647 Hom.: 28551

Bravo AF: 0.536

Asia WGS AF: 0.565 AC: 1967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10773983; hg19: chr12-1831246;