dbSNP rs17366568: ADIPOQ:c.-8-387G>A (chr3-186852664-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_004797.4(ADIPOQ):c.-8-387G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0912 in 219,184 control chromosomes in the GnomAD database, including 1,200 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 0.088 ( 819 hom., cov: 32)

Exomes 𝑓: 0.098 ( 381 hom. )

Consequence

ADIPOQ
NM_004797.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.07

Publications

98 publications found

Variant links:

Genes affected

ADIPOQ (HGNC:13633): (adiponectin, C1Q and collagen domain containing) This gene is expressed in adipose tissue exclusively. It encodes a protein with similarity to collagens X and VIII and complement factor C1q. The encoded protein circulates in the plasma and is involved with metabolic and hormonal processes. Mutations in this gene are associated with adiponectin deficiency. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Apr 2010]

ADIPOQ links:

ADIPOQ-AS1 (HGNC:40648): (ADIPOQ antisense RNA 1)

ADIPOQ-AS1 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=-0.79).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ADIPOQ	NM_004797.4 link	c.-8-387G>A	intron_variant	Intron 1 of 2	ENST00000320741.7	NP_004788.1	Q15848A8K660
ADIPOQ-AS1	NR_046662.2 link	n.2794C>T	non_coding_transcript_exon_variant	Exon 4 of 4
ADIPOQ	NM_001177800.2 link	c.-8-387G>A	intron_variant	Intron 2 of 3		NP_001171271.1	Q15848A8K660B2R773

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ADIPOQ	ENST00000320741.7 link	c.-8-387G>A	intron_variant	Intron 1 of 2	1	NM_004797.4	ENSP00000320709.2	Q15848
ADIPOQ	ENST00000444204.2 link	c.-8-387G>A	intron_variant	Intron 2 of 3	1		ENSP00000389814.2	Q15848
ADIPOQ-AS1	ENST00000422718.1 link	n.2665C>T	non_coding_transcript_exon_variant	Exon 3 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.0882

AC:

13427

AN:

152158

Hom.:

820

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0210

Gnomad AMI

AF:

0.281

Gnomad AMR

AF:

0.0690

Gnomad ASJ

AF:

0.144

Gnomad EAS

AF:

0.0297

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.137

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.0971

GnomAD4 exome

AF:

0.0979

AC:

6553

AN:

66908

Hom.:

381

Cov.:

AF XY:

0.100

AC XY:

3489

AN XY:

34798

show subpopulations

African (AFR)

AF:

0.0199

AC:

AN:

2362

American (AMR)

AF:

0.0596

AC:

249

AN:

4176

Ashkenazi Jewish (ASJ)

AF:

0.121

AC:

229

AN:

1898

East Asian (EAS)

AF:

0.0241

AC:

107

AN:

4446

South Asian (SAS)

AF:

0.117

AC:

433

AN:

3702

European-Finnish (FIN)

AF:

0.130

AC:

620

AN:

4768

Middle Eastern (MID)

AF:

0.102

AC:

AN:

284

European-Non Finnish (NFE)

AF:

0.108

AC:

4460

AN:

41476

Other (OTH)

AF:

0.0998

AC:

379

AN:

3796

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

281

562

842

1123

1404

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

168

210

<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:

0.0882

AC:

13427

AN:

152276

Hom.:

819

Cov.:

AF XY:

0.0903

AC XY:

6719

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.0210

AC:

871

AN:

41560

American (AMR)

AF:

0.0689

AC:

1054

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.144

AC:

498

AN:

3468

East Asian (EAS)

AF:

0.0297

AC:

154

AN:

5178

South Asian (SAS)

AF:

0.138

AC:

667

AN:

4824

European-Finnish (FIN)

AF:

0.137

AC:

1455

AN:

10614

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.121

AC:

8209

AN:

68012

Other (OTH)

AF:

0.0975

AC:

206

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

610

1220

1830

2440

3050

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

150

300

450

600

750

<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:

0.113

Hom.:

3853

Bravo

AF:

0.0792

Asia WGS

AF:

0.0710

AC:

249

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

5.4

(source)

DANN

Benign

0.61

PhyloP100

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