NM_024551.3:c.1032+902G>T

Variant names:

• chr12-1784975-G-T
• rs3809266
• NM_024551.3:c.1032+902G>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.1032+902G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,012 control chromosomes in the GnomAD database, including 8,163 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 (8163 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.170
• Publications: 6 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.1032+902G>T		intron_variant	Intron 7 of 7	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.1032+902G>T		intron_variant	Intron 7 of 7	1	NM_024551.3	ENSP00000349616.4

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47487 AN: 151894 Hom.: 8158 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.313 AC: 47523 AN: 152012 Hom.: 8163 Cov.: 32 AF XY: 0.320 AC XY: 23754 AN XY: 74292

African (AFR) AF: 0.197 AC: 8179 AN: 41500

American (AMR) AF: 0.480 AC: 7335 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1211 AN: 3460

East Asian (EAS) AF: 0.494 AC: 2549 AN: 5156

South Asian (SAS) AF: 0.399 AC: 1920 AN: 4816

European-Finnish (FIN) AF: 0.369 AC: 3885 AN: 10536

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21246 AN: 67954

Other (OTH) AF: 0.360 AC: 759 AN: 2110

Alfa AF: 0.290 Hom.: 987

Bravo AF: 0.320

Asia WGS AF: 0.433 AC: 1501 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.35
PhyloP100		-0.17
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: rs3809266; hg19: chr12-1894141;