dbSNP rs9882205: ADIPOQ:c.-8-442G>A (chr3-186852609-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.-8-442G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 183,710 control chromosomes in the GnomAD database, including 7,915 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 0.29 ( 6624 hom., cov: 32)

Exomes 𝑓: 0.27 ( 1291 hom. )

Consequence

ADIPOQ
NM_004797.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19

Publications

6 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ADIPOQ	NM_004797.4 link	c.-8-442G>A	intron_variant	Intron 1 of 2	ENST00000320741.7	NP_004788.1	Q15848A8K660
ADIPOQ-AS1	NR_046662.2 link	n.2849C>T	non_coding_transcript_exon_variant	Exon 4 of 4
ADIPOQ	NM_001177800.2 link	c.-8-442G>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.-8-442G>A	intron_variant	Intron 1 of 2	1	NM_004797.4	ENSP00000320709.2	Q15848
ADIPOQ	ENST00000444204.2 link	c.-8-442G>A	intron_variant	Intron 2 of 3	1		ENSP00000389814.2	Q15848
ADIPOQ-AS1	ENST00000422718.1 link	n.2720C>T	non_coding_transcript_exon_variant	Exon 3 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.285

AC:

43281

AN:

151916

Hom.:

6619

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.292

Gnomad AMR

AF:

0.300

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.596

Gnomad SAS

AF:

0.460

Gnomad FIN

AF:

0.259

Gnomad MID

AF:

0.405

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.329

GnomAD4 exome

AF:

0.266

AC:

8432

AN:

31676

Hom.:

1291

Cov.:

AF XY:

0.275

AC XY:

4497

AN XY:

16376

show subpopulations

African (AFR)

AF:

0.183

AC:

143

AN:

782

American (AMR)

AF:

0.249

AC:

793

AN:

3182

Ashkenazi Jewish (ASJ)

AF:

0.258

AC:

163

AN:

632

East Asian (EAS)

AF:

0.512

AC:

899

AN:

1756

South Asian (SAS)

AF:

0.404

AC:

868

AN:

2148

European-Finnish (FIN)

AF:

0.212

AC:

442

AN:

2080

Middle Eastern (MID)

AF:

0.349

AC:

AN:

European-Non Finnish (NFE)

AF:

0.241

AC:

4670

AN:

19342

Other (OTH)

AF:

0.254

AC:

424

AN:

1668

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

279

559

838

1118

1397

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

168

252

336

420

<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:

0.285

AC:

43334

AN:

152034

Hom.:

6624

Cov.:

AF XY:

0.292

AC XY:

21721

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.229

AC:

9503

AN:

41472

American (AMR)

AF:

0.300

AC:

4575

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.315

AC:

1093

AN:

3468

East Asian (EAS)

AF:

0.595

AC:

3058

AN:

5142

South Asian (SAS)

AF:

0.460

AC:

2213

AN:

4814

European-Finnish (FIN)

AF:

0.259

AC:

2744

AN:

10576

Middle Eastern (MID)

AF:

0.418

AC:

123

AN:

294

European-Non Finnish (NFE)

AF:

0.280

AC:

19055

AN:

67992

Other (OTH)

AF:

0.334

AC:

704

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1557

3115

4672

6230

7787

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

456

912

1368

1824

2280

<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:

0.284

Hom.:

9707

Bravo

AF:

0.281

Asia WGS

AF:

0.512

AC:

1780

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.054

(source)

DANN

Benign

0.41

PhyloP100

-1.2

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