rs1058322

Variant names:

• chr12-1727813-C-T
• rs1058322
• NM_024551.3:c.-86-26445C>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.-86-26445C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,210 control chromosomes in the GnomAD database, including 7,127 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 0.30 (7127 hom., cov: 28)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984
• Publications: 11 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.-86-26445C>T		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.-86-26445C>T		intron_variant	Intron 1 of 7	1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	n.145-26445C>T		intron_variant	Intron 1 of 2	3
ADIPOR2	ENST00000540974.1	n.149-2912C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45597 AN: 151094 Hom.: 7126 Cov.: 28

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.302 AC: 45621 AN: 151210 Hom.: 7127 Cov.: 28 AF XY: 0.304 AC XY: 22396 AN XY: 73774

African (AFR) AF: 0.271 AC: 11149 AN: 41214

American (AMR) AF: 0.350 AC: 5303 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1225 AN: 3470

East Asian (EAS) AF: 0.110 AC: 566 AN: 5146

South Asian (SAS) AF: 0.304 AC: 1454 AN: 4784

European-Finnish (FIN) AF: 0.320 AC: 3308 AN: 10330

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21655 AN: 67804

Other (OTH) AF: 0.325 AC: 681 AN: 2096

Alfa AF: 0.308 Hom.: 14225

Bravo AF: 0.303

Asia WGS AF: 0.220 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.48
PhyloP100		-0.98
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: rs1058322; hg19: chr12-1836979;