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:

Genome browser will be placed here

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.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADIPOR2	NM_024551.3	MANE Select	c.464-335T>G	intron	N/A	NP_078827.2
ADIPOR2	NM_001375363.1		c.464-335T>G	intron	N/A	NP_001362292.1
ADIPOR2	NM_001375364.1		c.464-335T>G	intron	N/A	NP_001362293.1	Q86V24

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADIPOR2	ENST00000357103.5	TSL:1 MANE Select	c.464-335T>G	intron	N/A	ENSP00000349616.4	Q86V24
ADIPOR2	ENST00000878990.1		c.542-335T>G	intron	N/A	ENSP00000549049.1
ADIPOR2	ENST00000878964.1		c.464-335T>G	intron	N/A	ENSP00000549023.1

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over