NM_024551.3:c.*1718C>T

Variant names:

• chr12-1787790-C-T
• rs1044471
• NM_024551.3:c.*1718C>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.*1718C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 152,128 control chromosomes in the GnomAD database, including 12,407 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 0.39 (12404 hom., cov: 32)
  • Exomes 𝑓: 0.40 (3 hom.)
• Consequence: ADIPOR2 NM_024551.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 42 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 (NFE) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024551.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	NM_024551.3	MANE Select	c.*1718C>T		3_prime_UTR	Exon 8 of 8	NP_078827.2
	ADIPOR2	NM_001375363.1		c.*1718C>T		3_prime_UTR	Exon 9 of 9	NP_001362292.1
	ADIPOR2	NM_001375364.1		c.*1718C>T		3_prime_UTR	Exon 9 of 9	NP_001362293.1	Q86V24

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOR2	ENST00000357103.5	TSL:1 MANE Select	c.*1718C>T		3_prime_UTR	Exon 8 of 8	ENSP00000349616.4	Q86V24
	ADIPOR2	ENST00000878990.1		c.*1718C>T		3_prime_UTR	Exon 10 of 10	ENSP00000549049.1
	ADIPOR2	ENST00000878964.1		c.*1718C>T		3_prime_UTR	Exon 9 of 9	ENSP00000549023.1

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58853 AN: 151980 Hom.: 12402 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.384

GnomAD4 exome AF: 0.400 AC: 12 AN: 30 Hom.: 3 Cov.: 0 AF XY: 0.500 AC XY: 8 AN XY: 16

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.563 AC: 9 AN: 16

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.333 AC: 2 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.387 AC: 58869 AN: 152098 Hom.: 12404 Cov.: 32 AF XY: 0.386 AC XY: 28724 AN XY: 74332

African (AFR) AF: 0.215 AC: 8906 AN: 41498

American (AMR) AF: 0.352 AC: 5381 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1615 AN: 3470

East Asian (EAS) AF: 0.403 AC: 2083 AN: 5170

South Asian (SAS) AF: 0.410 AC: 1976 AN: 4816

European-Finnish (FIN) AF: 0.452 AC: 4771 AN: 10564

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32767 AN: 67974

Other (OTH) AF: 0.386 AC: 815 AN: 2114

Alfa AF: 0.449 Hom.: 32237

Bravo AF: 0.370

Asia WGS AF: 0.378 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.46
PhyloP100		-0.10
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: rs1044471; hg19: chr12-1896956;