12-1719361-C-T

Variant names:

• chr12-1719361-C-T
• rs11061946
• NM_024551.3:c.-87+28170C>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+28170C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0721 in 152,132 control chromosomes in the GnomAD database, including 630 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 0.072 (630 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 13 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.-87+28170C>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+28170C>T		intron_variant	Intron 1 of 7	1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	n.144+30644C>T		intron_variant	Intron 1 of 2	3
ADIPOR2	ENST00000540974.1	n.149-11364C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0721 AC: 10957 AN: 152014 Hom.: 630 Cov.: 32

Gnomad AFR AF: 0.0150

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.0864

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0690

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0723

Gnomad OTH AF: 0.0887

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

GnomAD4 genome AF: 0.0721 AC: 10968 AN: 152132 Hom.: 630 Cov.: 32 AF XY: 0.0749 AC XY: 5569 AN XY: 74360

African (AFR) AF: 0.0149 AC: 619 AN: 41526

American (AMR) AF: 0.145 AC: 2220 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0864 AC: 300 AN: 3472

East Asian (EAS) AF: 0.258 AC: 1336 AN: 5170

South Asian (SAS) AF: 0.112 AC: 539 AN: 4818

European-Finnish (FIN) AF: 0.0690 AC: 729 AN: 10566

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0723 AC: 4918 AN: 67992

Other (OTH) AF: 0.0901 AC: 190 AN: 2108

Alfa AF: 0.0774 Hom.: 159

Bravo AF: 0.0788

Asia WGS AF: 0.172 AC: 594 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.9
DANN	Benign	0.56
PhyloP100		-0.36
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: rs11061946; hg19: chr12-1828527;