Genetic Variant NM_024551.3:c.870C>A (chr12-1783911-C-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4BP7BA1

The NM_024551.3(ADIPOR2):c.870C>A(p.Ile290Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 1,610,708 control chromosomes in the GnomAD database, including 12,291 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 0.13 ( 1511 hom., cov: 32)

Exomes 𝑓: 0.12 ( 10780 hom. )

Consequence

ADIPOR2
NM_024551.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.66

Publications

16 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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.15).

BP7

Synonymous conserved (PhyloP=1.66 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR2	NM_024551.3 link	c.870C>A	p.Ile290Ile	synonymous_variant	Exon 7 of 8	ENST00000357103.5	NP_078827.2	Q86V24

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOR2	ENST00000357103.5 link	c.870C>A	p.Ile290Ile	synonymous_variant	Exon 7 of 8	1	NM_024551.3	ENSP00000349616.4		Q86V24

Frequencies

GnomAD3 genomes

AF:

0.133

AC:

20255

AN:

151856

Hom.:

1511

Cov.:

show subpopulations

Gnomad AFR

AF:

0.194

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.0843

Gnomad ASJ

AF:

0.0906

Gnomad EAS

AF:

0.0249

Gnomad SAS

AF:

0.0741

Gnomad FIN

AF:

0.0988

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.130

GnomAD2 exomes

AF:

0.104

AC:

25945

AN:

248962

AF XY:

0.103

show subpopulations

Gnomad AFR exome

AF:

0.197

Gnomad AMR exome

AF:

0.0566

Gnomad ASJ exome

AF:

0.0956

Gnomad EAS exome

AF:

0.0266

Gnomad FIN exome

AF:

0.0984

Gnomad NFE exome

AF:

0.128

Gnomad OTH exome

AF:

0.107

GnomAD4 exome

AF:

0.118

AC:

172012

AN:

1458734

Hom.:

10780

Cov.:

AF XY:

0.117

AC XY:

84573

AN XY:

725702

show subpopulations

African (AFR)

AF:

0.198

AC:

6594

AN:

33320

American (AMR)

AF:

0.0593

AC:

2631

AN:

44378

Ashkenazi Jewish (ASJ)

AF:

0.0951

AC:

2469

AN:

25958

East Asian (EAS)

AF:

0.0155

AC:

613

AN:

39642

South Asian (SAS)

AF:

0.0753

AC:

6465

AN:

85886

European-Finnish (FIN)

AF:

0.102

AC:

5468

AN:

53358

Middle Eastern (MID)

AF:

0.0924

AC:

532

AN:

5760

European-Non Finnish (NFE)

AF:

0.127

AC:

140705

AN:

1110126

Other (OTH)

AF:

0.108

AC:

6535

AN:

60306

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

7709

15418

23128

30837

38546

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5016

10032

15048

20064

25080

<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:

0.133

AC:

20265

AN:

151974

Hom.:

1511

Cov.:

AF XY:

0.130

AC XY:

9655

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.194

AC:

8048

AN:

41416

American (AMR)

AF:

0.0841

AC:

1283

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.0906

AC:

314

AN:

3466

East Asian (EAS)

AF:

0.0244

AC:

126

AN:

5174

South Asian (SAS)

AF:

0.0746

AC:

357

AN:

4788

European-Finnish (FIN)

AF:

0.0988

AC:

1046

AN:

10586

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.129

AC:

8770

AN:

67968

Other (OTH)

AF:

0.128

AC:

270

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

869

1737

2606

3474

4343

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

214

428

642

856

1070

<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:

0.131

Hom.:

605

Bravo

AF:

0.135

Asia WGS

AF:

0.0520

AC:

183

AN:

3478

EpiCase

AF:

0.126

EpiControl

AF:

0.119

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.15

CADD

Benign

(source)

DANN

Benign

0.81

PhyloP100

1.7

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