NM_024551.3:c.*2046A>T

Variant names:

• chr12-1788118-A-T
• rs2286380
• NM_024551.3:c.*2046A>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.*2046A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,820 control chromosomes in the GnomAD database, including 1,594 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 0.14 (1594 hom., cov: 33)
  • Exomes 𝑓: 0.085 (0 hom.)
• Consequence: ADIPOR2 NM_024551.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 9 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 (AFR) allele frequency at 95% confidence interval = 0.2 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	NM_024551.3	MANE Select	c.*2046A>T		3_prime_UTR	Exon 8 of 8	NP_078827.2
	ADIPOR2	NM_001375363.1		c.*2046A>T		3_prime_UTR	Exon 9 of 9	NP_001362292.1
	ADIPOR2	NM_001375364.1		c.*2046A>T		3_prime_UTR	Exon 9 of 9	NP_001362293.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	ENST00000357103.5	TSL:1 MANE Select	c.*2046A>T		3_prime_UTR	Exon 8 of 8	ENSP00000349616.4

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20615 AN: 152170 Hom.: 1594 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.0844

Gnomad ASJ AF: 0.0908

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.0743

Gnomad FIN AF: 0.0990

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.0846 AC: 45 AN: 532 Hom.: 0 Cov.: 0 AF XY: 0.0898 AC XY: 30 AN XY: 334

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0953 AC: 41 AN: 430

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0385 AC: 3 AN: 78

Other (OTH) AF: 0.0556 AC: 1 AN: 18

GnomAD4 genome AF: 0.135 AC: 20625 AN: 152288 Hom.: 1594 Cov.: 33 AF XY: 0.132 AC XY: 9829 AN XY: 74482

African (AFR) AF: 0.203 AC: 8450 AN: 41546

American (AMR) AF: 0.0841 AC: 1287 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0908 AC: 315 AN: 3470

East Asian (EAS) AF: 0.0243 AC: 126 AN: 5192

South Asian (SAS) AF: 0.0748 AC: 361 AN: 4826

European-Finnish (FIN) AF: 0.0990 AC: 1052 AN: 10622

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8715 AN: 68018

Other (OTH) AF: 0.127 AC: 268 AN: 2110

Alfa AF: 0.129 Hom.: 195

Bravo AF: 0.137

Asia WGS AF: 0.0520 AC: 183 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	6.3
DANN	Benign	0.60
PhyloP100		0.010
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs2286380; hg19: chr12-1897284;