rs11836547

chr12-1777281-G-C

Variant summary

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

The NM_024551.3(ADIPOR2):c.292-573G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0703 in 151,700 control chromosomes in the GnomAD database, including 991 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 0.070 (991 hom., cov: 31)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADIPOR2	NM_024551.3	c.292-573G>C		intron_variant		ENST00000357103.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.292-573G>C		intron_variant		1	NM_024551.3	P1
ADIPOR2	ENST00000535774.1	n.249-573G>C		intron_variant, non_coding_transcript_variant		4
ADIPOR2	ENST00000543456.1	n.373-573G>C		intron_variant, non_coding_transcript_variant		3
ADIPOR2	ENST00000544470.1	n.40-573G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0700 AC: 10619 AN: 151592 Hom.: 987 Cov.: 31

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0387

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.0796

Gnomad SAS AF: 0.0816

Gnomad FIN AF: 0.00287

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00514

Gnomad OTH AF: 0.0628

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

GnomAD4 genome AF: 0.0703 AC: 10657 AN: 151700 Hom.: 991 Cov.: 31 AF XY: 0.0707 AC XY: 5242 AN XY: 74094

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.0386

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.0800

Gnomad4 SAS AF: 0.0816

Gnomad4 FIN AF: 0.00287

Gnomad4 NFE AF: 0.00514

Gnomad4 OTH AF: 0.0636

Alfa AF: 0.0429 Hom.: 86

Bravo AF: 0.0767

Asia WGS AF: 0.102 AC: 354 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.1
Dann	Benign	0.47

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: rs11836547; hg19: chr12-1886447;