NM_024551.3:c.172-3854T>A

Variant names:

• chr12-1768988-T-A
• rs4766415
• NM_024551.3:c.172-3854T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024551.3(ADIPOR2):​c.172-3854T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,084 control chromosomes in the GnomAD database, including 13,795 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 0.38 (13795 hom., cov: 32)
• Consequence: ADIPOR2 NM_024551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 11 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3	c.172-3854T>A		intron_variant	Intron 2 of 7	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5	c.172-3854T>A		intron_variant	Intron 2 of 7	1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000537545.1	n.402-3854T>A		intron_variant	Intron 2 of 2	3
ADIPOR2	ENST00000543456.1	n.253-3854T>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58409 AN: 151966 Hom.: 13795 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.384 AC: 58410 AN: 152084 Hom.: 13795 Cov.: 32 AF XY: 0.384 AC XY: 28549 AN XY: 74300

African (AFR) AF: 0.104 AC: 4317 AN: 41526

American (AMR) AF: 0.358 AC: 5473 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1637 AN: 3468

East Asian (EAS) AF: 0.402 AC: 2077 AN: 5172

South Asian (SAS) AF: 0.418 AC: 2017 AN: 4822

European-Finnish (FIN) AF: 0.518 AC: 5456 AN: 10532

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.529 AC: 35973 AN: 67962

Other (OTH) AF: 0.371 AC: 784 AN: 2114

Alfa AF: 0.453 Hom.: 2205

Bravo AF: 0.358

Asia WGS AF: 0.373 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.75
PhyloP100		-0.057
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: rs4766415; hg19: chr12-1878154;