Genetic Variant ADIPOR2:c.171+48A>T (chr12-1754562-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024551.3(ADIPOR2):c.171+48A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 1,544,186 control chromosomes in the GnomAD database, including 181,078 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 0.54 ( 23076 hom., cov: 31)

Exomes 𝑓: 0.47 ( 158002 hom. )

Consequence

ADIPOR2
NM_024551.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.109

Publications

19 publications found

Variant links:

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]

ADIPOR2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3 link	c.171+48A>T		intron_variant	Intron 2 of 7	ENST00000357103.5	NP_078827.2	Q86V24

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5 link	c.171+48A>T		intron_variant	Intron 2 of 7	1	NM_024551.3	ENSP00000349616.4		Q86V24
ADIPOR2	ENST00000537545.1 link	n.401+48A>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.541

AC:

82087

AN:

151778

Hom.:

23036

Cov.:

show subpopulations

Gnomad AFR

AF:

0.685

Gnomad AMI

AF:

0.390

Gnomad AMR

AF:

0.610

Gnomad ASJ

AF:

0.482

Gnomad EAS

AF:

0.598

Gnomad SAS

AF:

0.557

Gnomad FIN

AF:

0.469

Gnomad MID

AF:

0.528

Gnomad NFE

AF:

0.448

Gnomad OTH

AF:

0.569

GnomAD2 exomes

AF:

0.522

AC:

106629

AN:

204448

AF XY:

0.514

show subpopulations

Gnomad AFR exome

AF:

0.702

Gnomad AMR exome

AF:

0.626

Gnomad ASJ exome

AF:

0.484

Gnomad EAS exome

AF:

0.609

Gnomad FIN exome

AF:

0.481

Gnomad NFE exome

AF:

0.454

Gnomad OTH exome

AF:

0.517

GnomAD4 exome

AF:

0.472

AC:

657127

AN:

1392292

Hom.:

158002

Cov.:

AF XY:

0.472

AC XY:

325279

AN XY:

688652

show subpopulations

African (AFR)

AF:

0.694

AC:

21334

AN:

30734

American (AMR)

AF:

0.621

AC:

23352

AN:

37590

Ashkenazi Jewish (ASJ)

AF:

0.473

AC:

11353

AN:

24014

East Asian (EAS)

AF:

0.589

AC:

21842

AN:

37088

South Asian (SAS)

AF:

0.553

AC:

41346

AN:

74752

European-Finnish (FIN)

AF:

0.478

AC:

24550

AN:

51364

Middle Eastern (MID)

AF:

0.499

AC:

2674

AN:

5360

European-Non Finnish (NFE)

AF:

0.449

AC:

482639

AN:

1074012

Other (OTH)

AF:

0.489

AC:

28037

AN:

57378

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

17221

34441

51662

68882

86103

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.541

AC:

82181

AN:

151894

Hom.:

23076

Cov.:

AF XY:

0.544

AC XY:

40418

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.685

AC:

28361

AN:

41388

American (AMR)

AF:

0.610

AC:

9313

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.482

AC:

1672

AN:

3472

East Asian (EAS)

AF:

0.597

AC:

3089

AN:

5172

South Asian (SAS)

AF:

0.556

AC:

2675

AN:

4808

European-Finnish (FIN)

AF:

0.469

AC:

4943

AN:

10532

Middle Eastern (MID)

AF:

0.517

AC:

152

AN:

294

European-Non Finnish (NFE)

AF:

0.448

AC:

30424

AN:

67942

Other (OTH)

AF:

0.568

AC:

1196

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

1839

3678

5516

7355

9194

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.476

Hom.:

3269

Bravo

AF:

0.560

Asia WGS

AF:

0.598

AC:

2075

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

2.2

(source)

DANN

Benign

0.44

PhyloP100

0.11

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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12-1754562-A-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over