chr12-1787613-G-A

Variant names:

• chr12-1787613-G-A
• rs2286382
• NM_024551.3:c.*1541G>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.*1541G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0449 in 152,242 control chromosomes in the GnomAD database, including 263 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 0.045 (263 hom., cov: 32)
  • Exomes 𝑓: 0.38 (0 hom.)
• Consequence: ADIPOR2 NM_024551.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.354
• Publications: 5 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=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.*1541G>A		3_prime_UTR_variant	Exon 8 of 8	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.*1541G>A		3_prime_UTR_variant	Exon 8 of 8	1	NM_024551.3	ENSP00000349616.4

Frequencies

GnomAD3 genomes AF: 0.0448 AC: 6819 AN: 152116 Hom.: 263 Cov.: 32

Gnomad AFR AF: 0.0453

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0343

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.0496

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0261

Gnomad OTH AF: 0.0431

GnomAD4 exome AF: 0.375 AC: 3 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0449 AC: 6834 AN: 152234 Hom.: 263 Cov.: 32 AF XY: 0.0490 AC XY: 3645 AN XY: 74424

African (AFR) AF: 0.0455 AC: 1890 AN: 41554

American (AMR) AF: 0.0343 AC: 525 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.00576 AC: 20 AN: 3470

East Asian (EAS) AF: 0.188 AC: 974 AN: 5174

South Asian (SAS) AF: 0.0492 AC: 237 AN: 4818

European-Finnish (FIN) AF: 0.124 AC: 1314 AN: 10576

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0261 AC: 1775 AN: 68022

Other (OTH) AF: 0.0450 AC: 95 AN: 2112

Alfa AF: 0.0259 Hom.: 23

Bravo AF: 0.0390

Asia WGS AF: 0.119 AC: 412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.5
DANN	Benign	0.77
PhyloP100		-0.35
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: rs2286382; hg19: chr12-1896779;