Genetic Variant ADIPOR1:c.618-131G>A (chr1-202944076-C-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_015999.6(ADIPOR1):c.618-131G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0369 in 783,698 control chromosomes in the GnomAD database, including 2,224 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 0.076 ( 1117 hom., cov: 33)

Exomes 𝑓: 0.027 ( 1107 hom. )

Consequence

ADIPOR1
NM_015999.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.405

Publications

5 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=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOR1	NM_015999.6 link	c.618-131G>A		intron_variant	Intron 5 of 7	ENST00000340990.10	NP_057083.2	Q96A54

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ADIPOR1	ENST00000340990.10 link	c.618-131G>A	intron_variant	Intron 5 of 7	1	NM_015999.6	ENSP00000341785.5	Q96A54
ADIPOR1	ENST00000367254.7 link	c.431-213G>A	intron_variant	Intron 4 of 6	1		ENSP00000356223.3	F8W782
ADIPOR1	ENST00000495562.5 link	n.721G>A	non_coding_transcript_exon_variant	Exon 1 of 3	2
ADIPOR1	ENST00000417068.5 link	c.618-131G>A	intron_variant	Intron 6 of 6	3		ENSP00000402178.1	C9JNM5

Frequencies

GnomAD3 genomes

AF:

0.0759

AC:

11553

AN:

152140

Hom.:

1105

Cov.:

show subpopulations

Gnomad AFR

AF:

0.212

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0368

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.211

Gnomad SAS

AF:

0.0982

Gnomad FIN

AF:

0.00320

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.00660

Gnomad OTH

AF:

0.0611

GnomAD4 exome

AF:

0.0275

AC:

17347

AN:

631440

Hom.:

1107

Cov.:

AF XY:

0.0295

AC XY:

9536

AN XY:

323578

show subpopulations

African (AFR)

AF:

0.212

AC:

3294

AN:

15536

American (AMR)

AF:

0.0324

AC:

655

AN:

20192

Ashkenazi Jewish (ASJ)

AF:

0.00345

AC:

AN:

14778

East Asian (EAS)

AF:

0.154

AC:

4921

AN:

31930

South Asian (SAS)

AF:

0.0870

AC:

4240

AN:

48748

European-Finnish (FIN)

AF:

0.00254

AC:

100

AN:

39368

Middle Eastern (MID)

AF:

0.0269

AC:

AN:

2308

European-Non Finnish (NFE)

AF:

0.00650

AC:

2774

AN:

426866

Other (OTH)

AF:

0.0394

AC:

1250

AN:

31714

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

709

1419

2128

2838

3547

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

210

420

630

840

1050

<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:

0.0762

AC:

11595

AN:

152258

Hom.:

1117

Cov.:

AF XY:

0.0769

AC XY:

5725

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.212

AC:

8817

AN:

41528

American (AMR)

AF:

0.0369

AC:

565

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.00346

AC:

AN:

3470

East Asian (EAS)

AF:

0.211

AC:

1090

AN:

5172

South Asian (SAS)

AF:

0.0977

AC:

471

AN:

4822

European-Finnish (FIN)

AF:

0.00320

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00662

AC:

450

AN:

68018

Other (OTH)

AF:

0.0681

AC:

144

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

491

982

1474

1965

2456

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

240

360

480

600

<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:

0.0472

Hom.:

Bravo

AF:

0.0848

Asia WGS

AF:

0.157

AC:

545

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.3

(source)

DANN

Benign

0.38

PhyloP100

-0.41

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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