12-1722028-C-T

Position:

• chr12-1722028-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+30837C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0625 in 152,114 control chromosomes in the GnomAD database, including 464 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 0.062 (464 hom., cov: 31)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

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]

ADIPOR2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.-87+30837C>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+30837C>T		intron_variant		1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	n.145-32230C>T		intron_variant		3
ADIPOR2	ENST00000540974.1	n.149-8697C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0624 AC: 9477 AN: 151996 Hom.: 464 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0404

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.0521

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0262

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0625 AC: 9500 AN: 152114 Hom.: 464 Cov.: 31 AF XY: 0.0662 AC XY: 4926 AN XY: 74366

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0403

Gnomad4 ASJ AF: 0.00605

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.0517

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0262

Gnomad4 OTH AF: 0.0587

Alfa AF: 0.0309 Hom.: 65

Bravo AF: 0.0589

Asia WGS AF: 0.124 AC: 428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.1
DANN	Benign	0.68

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: rs11608456; hg19: chr12-1831194;