12-1695714-T-G

Position:

• chr12-1695714-T-G

Variant summary

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

The NM_024551.3(ADIPOR2):​c.-87+4523T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 151,514 control chromosomes in the GnomAD database, including 1,494 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 0.12 (1493 hom., cov: 31)
  • Exomes 𝑓: 0.13 (1 hom.)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

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]

ADIPOR2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.-87+4523T>G		intron_variant		ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.-87+4523T>G		intron_variant		1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	n.144+6997T>G		intron_variant		3
ADIPOR2	ENST00000540974.1	n.51+4501T>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18530 AN: 151368 Hom.: 1492 Cov.: 31

Gnomad AFR AF: 0.0373

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.0879

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.148

GnomAD4 exome AF: 0.125 AC: 4 AN: 32 Hom.: 1 AF XY: 0.167 AC XY: 4 AN XY: 24

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.0833

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.122 AC: 18544 AN: 151482 Hom.: 1493 Cov.: 31 AF XY: 0.124 AC XY: 9146 AN XY: 73968

Gnomad4 AFR AF: 0.0373

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.0879

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.149

Alfa AF: 0.0955 Hom.: 212

Bravo AF: 0.131

Asia WGS AF: 0.207 AC: 716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.32

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: rs2058033; hg19: chr12-1804880;