chr12-1694068-C-T

Variant names:

• chr12-1694068-C-T
• rs11061925
• NM_024551.3:c.-87+2877C>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.-87+2877C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,986 control chromosomes in the GnomAD database, including 6,744 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 0.28 (6744 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.-87+2877C>T		intron_variant	Intron 1 of 7	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.-87+2877C>T		intron_variant	Intron 1 of 7	1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	n.144+5351C>T		intron_variant	Intron 1 of 2	3
ADIPOR2	ENST00000540974.1	n.51+2855C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43096 AN: 151868 Hom.: 6743 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.284 AC: 43105 AN: 151986 Hom.: 6744 Cov.: 32 AF XY: 0.286 AC XY: 21264 AN XY: 74294

African (AFR) AF: 0.169 AC: 7001 AN: 41436

American (AMR) AF: 0.451 AC: 6881 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1178 AN: 3472

East Asian (EAS) AF: 0.327 AC: 1689 AN: 5164

South Asian (SAS) AF: 0.347 AC: 1673 AN: 4820

European-Finnish (FIN) AF: 0.257 AC: 2698 AN: 10516

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.307 AC: 20867 AN: 67992

Other (OTH) AF: 0.320 AC: 677 AN: 2114

Alfa AF: 0.278 Hom.: 849

Bravo AF: 0.296

Asia WGS AF: 0.313 AC: 1086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.79
PhyloP100		-1.2
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: rs11061925; hg19: chr12-1803234;