Genetic Variant ADIPOR1:c.258+85C>G (chr1-202948219-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_015999.6(ADIPOR1):c.258+85C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0449 in 1,101,718 control chromosomes in the GnomAD database, including 1,461 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 0.042 ( 176 hom., cov: 32)

Exomes 𝑓: 0.045 ( 1285 hom. )

Consequence

ADIPOR1
NM_015999.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.686

Publications

4 publications found

Variant links:

Genes affected

ADIPOR1 (HGNC:24040): (adiponectin receptor 1) This gene encodes a protein which acts as a receptor for adiponectin, a hormone secreted by adipocytes which regulates fatty acid catabolism and glucose levels. Binding of adiponectin to the encoded protein results in activation of an AMP-activated kinase signaling pathway which affects levels of fatty acid oxidation and insulin sensitivity. A pseudogene of this gene is located on chromosome 14. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2014]

ADIPOR1 Gene-Disease associations (from GenCC):

retinitis pigmentosa
Inheritance: AD Classification: LIMITED Submitted by: Franklin by Genoox

ADIPOR1 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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR1	NM_015999.6 link	c.258+85C>G		intron_variant	Intron 3 of 7	ENST00000340990.10	NP_057083.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
ADIPOR1	ENST00000340990.10 link	c.258+85C>G	intron_variant	Intron 3 of 7	1	NM_015999.6	ENSP00000341785.5
ADIPOR1	ENST00000367254.7 link	c.258+85C>G	intron_variant	Intron 3 of 6	1		ENSP00000356223.3
ADIPOR1	ENST00000417068.5 link	c.258+85C>G	intron_variant	Intron 4 of 6	3		ENSP00000402178.1
ADIPOR1	ENST00000426229.1 link	c.258+85C>G	intron_variant	Intron 4 of 5	2		ENSP00000392946.1

Frequencies

GnomAD3 genomes

AF:

0.0417

AC:

6335

AN:

152080

Hom.:

172

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0427

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0240

Gnomad ASJ

AF:

0.0375

Gnomad EAS

AF:

0.112

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.0294

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0371

Gnomad OTH

AF:

0.0425

GnomAD4 exome

AF:

0.0454

AC:

43092

AN:

949520

Hom.:

1285

AF XY:

0.0475

AC XY:

22703

AN XY:

478374

show subpopulations

African (AFR)

AF:

0.0447

AC:

928

AN:

20742

American (AMR)

AF:

0.0203

AC:

503

AN:

24822

Ashkenazi Jewish (ASJ)

AF:

0.0408

AC:

675

AN:

16542

East Asian (EAS)

AF:

0.116

AC:

3888

AN:

33440

South Asian (SAS)

AF:

0.102

AC:

5913

AN:

58184

European-Finnish (FIN)

AF:

0.0334

AC:

1570

AN:

47076

Middle Eastern (MID)

AF:

0.0442

AC:

127

AN:

2872

European-Non Finnish (NFE)

AF:

0.0391

AC:

27507

AN:

703946

Other (OTH)

AF:

0.0473

AC:

1981

AN:

41896

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1931

3861

5792

7722

9653

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1004

2008

3012

4016

5020

<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:

0.0417

AC:

6352

AN:

152198

Hom.:

176

Cov.:

AF XY:

0.0422

AC XY:

3137

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.0431

AC:

1789

AN:

41506

American (AMR)

AF:

0.0240

AC:

367

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0375

AC:

130

AN:

3470

East Asian (EAS)

AF:

0.111

AC:

577

AN:

5184

South Asian (SAS)

AF:

0.113

AC:

544

AN:

4818

European-Finnish (FIN)

AF:

0.0294

AC:

311

AN:

10584

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0371

AC:

2523

AN:

68020

Other (OTH)

AF:

0.0421

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

304

608

913

1217

1521

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

264

352

440

<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:

0.0385

Hom.:

Bravo

AF:

0.0394

Asia WGS

AF:

0.113

AC:

394

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.12

(source)

DANN

Benign

0.44

PhyloP100

-0.69

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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