rs10773989

Positions:

• chr12-1747816-T-C

Variant summary

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

The ENST00000357103.5(ADIPOR2):​c.-86-6442T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,914 control chromosomes in the GnomAD database, including 13,918 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 0.42 (13918 hom., cov: 31)
• Consequence: ADIPOR2 ENST00000357103.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.-86-6442T>C		intron_variant		ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.-86-6442T>C		intron_variant		1	NM_024551.3	ENSP00000349616	P1
ADIPOR2	ENST00000537545.1	n.145-6442T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63219 AN: 151796 Hom.: 13909 Cov.: 31

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.416 AC: 63253 AN: 151914 Hom.: 13918 Cov.: 31 AF XY: 0.413 AC XY: 30702 AN XY: 74252

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.389

Alfa AF: 0.461 Hom.: 5110

Bravo AF: 0.402

Asia WGS AF: 0.437 AC: 1523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	12
DANN	Benign	0.53

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: rs10773989; hg19: chr12-1856982;