12-1766464-C-T

Variant names:

• chr12-1766464-C-T
• rs12813694
• NM_024551.3:c.172-6378C>T

Variant summary

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

The NM_024551.3(ADIPOR2):​c.172-6378C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,014 control chromosomes in the GnomAD database, including 8,137 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 0.31 (8137 hom., cov: 31)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 7 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024551.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	NM_024551.3	MANE Select	c.172-6378C>T		intron	N/A	NP_078827.2
	ADIPOR2	NM_001375363.1		c.172-6378C>T		intron	N/A	NP_001362292.1
	ADIPOR2	NM_001375364.1		c.172-6378C>T		intron	N/A	NP_001362293.1	Q86V24

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	ENST00000357103.5	TSL:1 MANE Select	c.172-6378C>T		intron	N/A	ENSP00000349616.4	Q86V24
	ADIPOR2	ENST00000878990.1		c.172-3122C>T		intron	N/A	ENSP00000549049.1
	ADIPOR2	ENST00000878964.1		c.172-6378C>T		intron	N/A	ENSP00000549023.1

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47351 AN: 151896 Hom.: 8133 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.312 AC: 47384 AN: 152014 Hom.: 8137 Cov.: 31 AF XY: 0.319 AC XY: 23677 AN XY: 74320

African (AFR) AF: 0.193 AC: 8015 AN: 41462

American (AMR) AF: 0.479 AC: 7310 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1220 AN: 3466

East Asian (EAS) AF: 0.495 AC: 2560 AN: 5176

South Asian (SAS) AF: 0.397 AC: 1918 AN: 4826

European-Finnish (FIN) AF: 0.368 AC: 3889 AN: 10558

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21277 AN: 67954

Other (OTH) AF: 0.358 AC: 753 AN: 2102

Alfa AF: 0.296 Hom.: 941

Bravo AF: 0.319

Asia WGS AF: 0.433 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.75
PhyloP100		-0.46
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: rs12813694; hg19: chr12-1875630;