chr12-1787714-C-T

Position:

• chr12-1787714-C-T

Variant summary

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

The NM_024551.3(ADIPOR2):​c.*1642C>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 0.313 in 152,086 control chromosomes in the GnomAD database, including 8,176 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 (8176 hom., cov: 32)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: ADIPOR2 NM_024551.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.*1642C>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.*1642C>T		3_prime_UTR_variant	8/8	1	NM_024551.3	ENSP00000349616.4

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47508 AN: 151962 Hom.: 8171 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.356

GnomAD4 exome AF: 0.333 AC: 2 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.313 AC: 47544 AN: 152080 Hom.: 8176 Cov.: 32 AF XY: 0.320 AC XY: 23772 AN XY: 74342

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.357

Alfa AF: 0.318 Hom.: 11196

Bravo AF: 0.320

Asia WGS AF: 0.431 AC: 1496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.58
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: rs12342; hg19: chr12-1896880;