12-1778532-C-T

Variant names:

• chr12-1778532-C-T
• rs2370055
• NM_024551.3:c.463+507C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375363.1(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_001375363.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375363.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	NM_024551.3	MANE Select	c.463+507C>T		intron	N/A	NP_078827.2
	ADIPOR2	NM_001375363.1		c.463+507C>T		intron	N/A	NP_001362292.1
	ADIPOR2	NM_001375364.1		c.463+507C>T		intron	N/A	NP_001362293.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	ENST00000357103.5	TSL:1 MANE Select	c.463+507C>T		intron	N/A	ENSP00000349616.4
	ADIPOR2	ENST00000878990.1		c.541+507C>T		intron	N/A	ENSP00000549049.1
	ADIPOR2	ENST00000878964.1		c.463+507C>T		intron	N/A	ENSP00000549023.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.276 AC: 16 AN: 58

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.151 AC: 6278 AN: 41452

American (AMR) AF: 0.446 AC: 6800 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1198 AN: 3464

East Asian (EAS) AF: 0.305 AC: 1578 AN: 5172

South Asian (SAS) AF: 0.348 AC: 1672 AN: 4798

European-Finnish (FIN) AF: 0.245 AC: 2574 AN: 10526

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19503 AN: 67926

Other (OTH) AF: 0.311 AC: 656 AN: 2106

Alfa AF: 0.253 Hom.: 729

Bravo AF: 0.281

Asia WGS AF: 0.312 AC: 1080 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.62
DANN	Benign	0.41
PhyloP100		-2.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2370055; hg19: chr12-1887698;