12-1690101-T-G

Variant names:

• chr12-1690101-T-G
• rs1029629
• ENST00000537545.1:n.144+1384T>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000537545.1	n.144+1384T>G		intron_variant	Intron 1 of 2	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;