rs11061925

Positions:

• chr12-1694068-C-T

Variant summary

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

The NM_024551.3(ADIPOR2):​c.-87+2877C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,986 control chromosomes in the GnomAD database, including 6,744 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 0.28 (6744 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

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 (AMR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.-87+2877C>T		intron_variant		ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.-87+2877C>T		intron_variant		1	NM_024551.3	ENSP00000349616	P1
ADIPOR2	ENST00000537545.1	n.144+5351C>T		intron_variant, non_coding_transcript_variant		3
ADIPOR2	ENST00000540974.1	n.51+2855C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43096 AN: 151868 Hom.: 6743 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.284 AC: 43105 AN: 151986 Hom.: 6744 Cov.: 32 AF XY: 0.286 AC XY: 21264 AN XY: 74294

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.320

Alfa AF: 0.281 Hom.: 824

Bravo AF: 0.296

Asia WGS AF: 0.313 AC: 1086 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	1.4
DANN	Benign	0.79

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: rs11061925; hg19: chr12-1803234;