rs1029629

Positions:

• chr12-1690101-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000537545.1(ADIPOR2):​n.144+1384T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,102 control chromosomes in the GnomAD database, including 7,464 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 0.31 (7464 hom., cov: 33)
• Consequence: ADIPOR2 ENST00000537545.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000537545.1	n.144+1384T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46535 AN: 151980 Hom.: 7461 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.306 AC: 46558 AN: 152102 Hom.: 7464 Cov.: 33 AF XY: 0.308 AC XY: 22930 AN XY: 74362

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.335

Alfa AF: 0.317 Hom.: 7472

Bravo AF: 0.322

Asia WGS AF: 0.326 AC: 1131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1029629; hg19: chr12-1799267;