12-1788118-A-T

Position:

• chr12-1788118-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.*2046A>T		3_prime_UTR_variant	8/8	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.*2046A>T		3_prime_UTR_variant	8/8	1	NM_024551.3	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

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0953

Gnomad4 NFE exome AF: 0.0385

Gnomad4 OTH exome AF: 0.0556

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

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.0841

Gnomad4 ASJ AF: 0.0908

Gnomad4 EAS AF: 0.0243

Gnomad4 SAS AF: 0.0748

Gnomad4 FIN AF: 0.0990

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.127

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.3
DANN	Benign	0.60
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Publications

LitVar

Other links and lift over

dbSNP: rs2286380; hg19: chr12-1897284;