dbSNP rs2275735: ADIPOR1:c.430+12G>A (chr1-202946427-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_015999.6(ADIPOR1):c.430+12G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0441 in 1,613,514 control chromosomes in the GnomAD database, including 2,054 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.042 ( 175 hom., cov: 31)

Exomes 𝑓: 0.044 ( 1879 hom. )

Consequence

ADIPOR1
NM_015999.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.295

Publications

12 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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 1-202946427-C-T is Benign according to our data. Variant chr1-202946427-C-T is described in ClinVar as Benign. ClinVar VariationId is 1168437.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015999.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADIPOR1	NM_015999.6	MANE Select	c.430+12G>A	intron	N/A	NP_057083.2
ADIPOR1	NM_001290553.2		c.430+12G>A	intron	N/A	NP_001277482.1	Q96A54
ADIPOR1	NM_001290557.1		c.430+12G>A	intron	N/A	NP_001277486.1	Q96A54

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADIPOR1	ENST00000340990.10	TSL:1 MANE Select	c.430+12G>A	intron	N/A	ENSP00000341785.5	Q96A54
ADIPOR1	ENST00000367254.7	TSL:1	c.430+12G>A	intron	N/A	ENSP00000356223.3	F8W782
ADIPOR1	ENST00000855702.1		c.430+12G>A	intron	N/A	ENSP00000525761.1

Frequencies

GnomAD3 genomes

AF:

0.0416

AC:

6317

AN:

151934

Hom.:

172

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0428

Gnomad AMI

AF:

0.0154

Gnomad AMR

AF:

0.0242

Gnomad ASJ

AF:

0.0375

Gnomad EAS

AF:

0.110

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.0292

Gnomad MID

AF:

0.0255

Gnomad NFE

AF:

0.0371

Gnomad OTH

AF:

0.0421

GnomAD2 exomes

AF:

0.0478

AC:

11987

AN:

250726

AF XY:

0.0511

show subpopulations

Gnomad AFR exome

AF:

0.0416

Gnomad AMR exome

AF:

0.0185

Gnomad ASJ exome

AF:

0.0412

Gnomad EAS exome

AF:

0.0951

Gnomad FIN exome

AF:

0.0320

Gnomad NFE exome

AF:

0.0382

Gnomad OTH exome

AF:

0.0440

GnomAD4 exome

AF:

0.0443

AC:

64798

AN:

1461462

Hom.:

1879

Cov.:

AF XY:

0.0464

AC XY:

33733

AN XY:

727030

show subpopulations

African (AFR)

AF:

0.0445

AC:

1490

AN:

33470

American (AMR)

AF:

0.0193

AC:

861

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.0411

AC:

1073

AN:

26126

East Asian (EAS)

AF:

0.114

AC:

4515

AN:

39690

South Asian (SAS)

AF:

0.101

AC:

8687

AN:

86224

European-Finnish (FIN)

AF:

0.0334

AC:

1781

AN:

53402

Middle Eastern (MID)

AF:

0.0431

AC:

242

AN:

5620

European-Non Finnish (NFE)

AF:

0.0389

AC:

43271

AN:

1111844

Other (OTH)

AF:

0.0477

AC:

2878

AN:

60368

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

2959

5917

8876

11834

14793

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1734

3468

5202

6936

8670

<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:

0.0416

AC:

6331

AN:

152052

Hom.:

175

Cov.:

AF XY:

0.0420

AC XY:

3119

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.0431

AC:

1786

AN:

41474

American (AMR)

AF:

0.0242

AC:

370

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0375

AC:

130

AN:

3470

East Asian (EAS)

AF:

0.109

AC:

563

AN:

5142

South Asian (SAS)

AF:

0.113

AC:

542

AN:

4816

European-Finnish (FIN)

AF:

0.0292

AC:

308

AN:

10564

Middle Eastern (MID)

AF:

0.0274

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0371

AC:

2522

AN:

67994

Other (OTH)

AF:

0.0417

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

302

604

905

1207

1509

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

258

344

430

<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:

0.0388

Hom.:

248

Bravo

AF:

0.0394

Asia WGS

AF:

0.110

AC:

385

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

7.5

(source)

DANN

Benign

0.57

PhyloP100

-0.29

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)

0.010

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