NM_024551.3:c.-86-13278G>A

Variant names:

• chr12-1740980-G-A
• rs12316367
• NM_024551.3:c.-86-13278G>A

Variant summary

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

The NM_024551.3(ADIPOR2):​c.-86-13278G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,084 control chromosomes in the GnomAD database, including 14,049 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 0.40 (14049 hom., cov: 31)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 3 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]

ENSG00000285627 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.-86-13278G>A		intron_variant	Intron 1 of 7	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.-86-13278G>A		intron_variant	Intron 1 of 7	1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	n.145-13278G>A		intron_variant	Intron 1 of 2	3
ENSG00000285627	ENST00000650086.1	n.*217C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61070 AN: 151966 Hom.: 14047 Cov.: 31

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.402 AC: 61078 AN: 152084 Hom.: 14049 Cov.: 31 AF XY: 0.401 AC XY: 29807 AN XY: 74336

African (AFR) AF: 0.172 AC: 7147 AN: 41504

American (AMR) AF: 0.366 AC: 5597 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1624 AN: 3472

East Asian (EAS) AF: 0.396 AC: 2043 AN: 5164

South Asian (SAS) AF: 0.420 AC: 2025 AN: 4816

European-Finnish (FIN) AF: 0.513 AC: 5421 AN: 10564

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35742 AN: 67966

Other (OTH) AF: 0.381 AC: 803 AN: 2110

Alfa AF: 0.451 Hom.: 6352

Bravo AF: 0.379

Asia WGS AF: 0.374 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.9
DANN	Benign	0.73
PhyloP100		1.0
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: rs12316367; hg19: chr12-1850146;