rs1342387

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The NM_015999.6(ADIPOR1):c.431-59A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a cumulative frequency of 0.543 (AC=769,944) in the gnomAD database across 1,418,200 control chromosomes, including 210,210 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.602. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.53 ( 21299 hom., cov: 32)

Exomes 𝑓: 0.54 ( 188911 hom. )

Consequence

ADIPOR1
NM_015999.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.66

Publications

71 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: SD, AD Classification: MODERATE, LIMITED Submitted by: PanelApp Australia, Franklin by Genoox

ADIPOR1 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_015999.6, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript

Our verdict: Benign. The variant received -12 points.

BP4

Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); Splicing verdict: benign (Strong).; Germline computational verdict: benign (Strong).

BA1

GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.6022 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

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

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADIPOR1	NM_015999.6	MANE Select	c.431-59A>G	intron	N/A	NP_057083.2
ADIPOR1	NM_001290553.2		c.431-59A>G	intron	N/A	NP_001277482.1	Q96A54
ADIPOR1	NM_001290557.1		c.431-59A>G	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.431-59A>G	intron	N/A	ENSP00000341785.5	Q96A54
ADIPOR1	ENST00000367254.7	TSL:1	c.430+1211A>G	intron	N/A	ENSP00000356223.3	F8W782
ADIPOR1	ENST00000855702.1		c.431-59A>G	intron	N/A	ENSP00000525761.1	Q96A54

Frequencies

GnomAD3 genomes

AF:

0.528

AC:

80196

AN:

151976

Hom.:

21263

Cov.:

show subpopulations

Gnomad AFR

AF:

0.521

Gnomad AMI

AF:

0.312

Gnomad AMR

AF:

0.484

Gnomad ASJ

AF:

0.471

Gnomad EAS

AF:

0.620

Gnomad SAS

AF:

0.520

Gnomad FIN

AF:

0.479

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.549

Gnomad OTH

AF:

0.528

GnomAD4 exome

AF:

0.545

AC:

689667

AN:

1266106

Hom.:

188911

AF XY:

0.544

AC XY:

337321

AN XY:

620224

show subpopulations

African (AFR)

AF:

0.516

AC:

14589

AN:

28280

American (AMR)

AF:

0.467

AC:

10146

AN:

21732

Ashkenazi Jewish (ASJ)

AF:

0.464

AC:

9136

AN:

19678

East Asian (EAS)

AF:

0.554

AC:

19960

AN:

36060

South Asian (SAS)

AF:

0.495

AC:

29390

AN:

59334

European-Finnish (FIN)

AF:

0.497

AC:

22534

AN:

45368

Middle Eastern (MID)

AF:

0.438

AC:

1526

AN:

3486

European-Non Finnish (NFE)

AF:

0.554

AC:

554546

AN:

1000298

Other (OTH)

AF:

0.537

AC:

27840

AN:

51870

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

14749

29497

44246

58994

73743

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16354

32708

49062

65416

81770

<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:

0.528

AC:

80277

AN:

152094

Hom.:

21299

Cov.:

AF XY:

0.525

AC XY:

39056

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.522

AC:

21633

AN:

41480

American (AMR)

AF:

0.484

AC:

7401

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.471

AC:

1634

AN:

3466

East Asian (EAS)

AF:

0.620

AC:

3207

AN:

5172

South Asian (SAS)

AF:

0.519

AC:

2501

AN:

4822

European-Finnish (FIN)

AF:

0.479

AC:

5062

AN:

10560

Middle Eastern (MID)

AF:

0.449

AC:

131

AN:

292

European-Non Finnish (NFE)

AF:

0.549

AC:

37299

AN:

67992

Other (OTH)

AF:

0.533

AC:

1125

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1966

3932

5899

7865

9831

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

712

1424

2136

2848

3560

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

TOPMed (Bravo)

AF:

0.526

AC:

139325

AN:

264690

Hom.:

36882

ALFA (dbGaP/dbSNP Allele Frequency Aggregator)

AF:

0.536

AC:

145530

AN:

271324

Hom.:

39098

Local populations

ABraOM SABE-WGS-1171

AF:

0.529

AC:

1240

AN:

2342

Hom.:

327

ChinaMAP Phase 1

AF:

0.636

Denmark Genome

AF:

0.517

AC:

155

AN:

300

GenomeAsia100K

AF:

0.578

AC:

2008

AN:

3478

show subpopulations

Oceania

AF:

0.905

AC:

134

AN:

148

Hom.:

North-East Asia

AF:

0.511

AC:

359

AN:

702

Hom.:

South-East Asia

AF:

0.676

AC:

468

AN:

692

Hom.:

159

South Asia

AF:

0.566

AC:

820

AN:

1448

Hom.:

240

Africa

AF:

0.481

AC:

100

AN:

208

Hom.:

America

AF:

0.308

AC:

AN:

Hom.:

West Eurasia

AF:

0.487

AC:

111

AN:

228

Hom.:

Korea4K (4,157 Koreans)

AF:

0.552

AC:

3995

AN:

7234

Qatari Genome

AF:

0.386

AC:

AN:

176

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.514

AC:

63052

AN:

122706

Hom.:

16282

Turkish Variome

AF:

0.462

AC:

715

AN:

1546

Hom.:

160

UK10K

AF:

0.560

AC:

4233

AN:

7562

show subpopulations

TwinsUK

AF:

0.546

AC:

1952

AN:

3574

ALSPAC

AF:

0.573

AC:

2207

AN:

3854

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.646

AC:

5785

AN:

8960

Hom.:

1883

Case/control cohorts

Cohort

Cases

Controls

SCHEMA

(Schizophrenia)

22130 / 54924AF: 0.402920

35817 / 91882AF: 0.389815

Allele count / allele number. AF is computed from the counts for ASC (not provided by the source).

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.52

(source)

DANN

Benign

0.66

PhyloP100

-1.7

AlphaGenome AVI

Benign

0.87

(source)

GPN-Star LLR

2.6

(source)

GPN-Star score

-1.3

(source)

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

Pangolin (max)

Benign

0.0

(source)

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

Local populations

Case/control cohorts

ClinVar

Computational scores

Splicing

Publications

Other links and lift over