Genetic Variant ADIPOR2:c.464-335T>G (chr12-1780116-T-G) – 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.464-335T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0507 in 183,788 control chromosomes in the GnomAD database, including 661 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 0.057 ( 633 hom., cov: 32)

Exomes 𝑓: 0.018 ( 28 hom. )

Consequence

ADIPOR2
NM_024551.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.104

Publications

4 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=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3 link	c.464-335T>G		intron_variant	Intron 4 of 7	ENST00000357103.5	NP_078827.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
ADIPOR2	ENST00000357103.5 link	c.464-335T>G	intron_variant	Intron 4 of 7	1	NM_024551.3	ENSP00000349616.4
ADIPOR2	ENST00000535774.1 link	n.421-335T>G	intron_variant	Intron 2 of 2	4
ADIPOR2	ENST00000537190.1 link	n.-32T>G	upstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.0572

AC:

8712

AN:

152178

Hom.:

635

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0316

Gnomad ASJ

AF:

0.0395

Gnomad EAS

AF:

0.0800

Gnomad SAS

AF:

0.0813

Gnomad FIN

AF:

0.00282

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.00494

Gnomad OTH

AF:

0.0512

GnomAD4 exome

AF:

0.0183

AC:

575

AN:

31492

Hom.:

Cov.:

AF XY:

0.0186

AC XY:

302

AN XY:

16204

show subpopulations

African (AFR)

AF:

0.150

AC:

175

AN:

1168

American (AMR)

AF:

0.0186

AC:

AN:

858

Ashkenazi Jewish (ASJ)

AF:

0.0369

AC:

AN:

1328

East Asian (EAS)

AF:

0.0480

AC:

AN:

1856

South Asian (SAS)

AF:

0.0595

AC:

AN:

840

European-Finnish (FIN)

AF:

0.00392

AC:

AN:

1532

Middle Eastern (MID)

AF:

0.0345

AC:

AN:

174

European-Non Finnish (NFE)

AF:

0.00440

AC:

AN:

21576

Other (OTH)

AF:

0.0412

AC:

AN:

2160

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

117

146

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0574

AC:

8737

AN:

152296

Hom.:

633

Cov.:

AF XY:

0.0584

AC XY:

4351

AN XY:

74488

show subpopulations

African (AFR)

AF:

0.164

AC:

6815

AN:

41542

American (AMR)

AF:

0.0316

AC:

483

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0395

AC:

137

AN:

3468

East Asian (EAS)

AF:

0.0803

AC:

417

AN:

5190

South Asian (SAS)

AF:

0.0814

AC:

393

AN:

4828

European-Finnish (FIN)

AF:

0.00282

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00494

AC:

336

AN:

68028

Other (OTH)

AF:

0.0521

AC:

110

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

384

768

1152

1536

1920

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

282

376

470

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0194

Hom.:

203

Bravo

AF:

0.0616

Asia WGS

AF:

0.101

AC:

350

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.6

(source)

DANN

Benign

0.80

PhyloP100

0.10

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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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