12-1778532-C-T

Position:

• chr12-1778532-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.463+507C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 151,970 control chromosomes in the GnomAD database, including 6,152 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 0.27 (6149 hom., cov: 32)
  • Exomes 𝑓: 0.27 (3 hom.)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.463+507C>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.463+507C>T		intron_variant		1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000544470.1	n.718C>T		non_coding_transcript_exon_variant	2/2	2
ADIPOR2	ENST00000535774.1	n.420+507C>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40675 AN: 151786 Hom.: 6152 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.313

GnomAD4 exome AF: 0.273 AC: 18 AN: 66 Hom.: 3 Cov.: 0 AF XY: 0.265 AC XY: 9 AN XY: 34

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.276

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.268 AC: 40696 AN: 151904 Hom.: 6149 Cov.: 32 AF XY: 0.271 AC XY: 20096 AN XY: 74236

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.311

Alfa AF: 0.257 Hom.: 713

Bravo AF: 0.281

Asia WGS AF: 0.312 AC: 1080 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.62
DANN	Benign	0.41

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: rs2370055; hg19: chr12-1887698;