chr12-1724622-G-A

Position:

• chr12-1724622-G-A

Variant summary

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

The NM_024551.3(ADIPOR2):​c.-86-29636G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,050 control chromosomes in the GnomAD database, including 36,685 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 0.69 (36685 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.-86-29636G>A		intron_variant		ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.-86-29636G>A		intron_variant		1	NM_024551.3	ENSP00000349616	P1
ADIPOR2	ENST00000537545.1	n.145-29636G>A		intron_variant, non_coding_transcript_variant		3
ADIPOR2	ENST00000540974.1	n.149-6103G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105046 AN: 151934 Hom.: 36648 Cov.: 32

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.691 AC: 105136 AN: 152050 Hom.: 36685 Cov.: 32 AF XY: 0.690 AC XY: 51315 AN XY: 74328

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.661

Alfa AF: 0.703 Hom.: 20226

Bravo AF: 0.674

Asia WGS AF: 0.676 AC: 2354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.67
DANN	Benign	0.42

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: rs4766413; hg19: chr12-1833788;