dbSNP rs822396: ADIPOQ:c.-8-3963G>A (chr3-186849088-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is The variant received -4 classification points (ACGS-UK Somatic Oncogenicity v2025): 0P and 4B. B1_Strong

The NM_004797.4(ADIPOQ):c.-8-3963G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The gene ADIPOQ is a tumor suppressor gene (CancerMine: 2 TSG, 6 oncogene citations). The gene ADIPOQ is a known oncogene (CancerMine: 2 TSG, 6 oncogene citations). The variant allele was found at a cumulative frequency of 0.813 (AC=123,746) in the gnomAD database across 152,116 control chromosomes, including 50,365 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.869. 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 0.81 ( 50365 hom., cov: 31)

Consequence

ADIPOQ
NM_004797.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.976

Publications

106 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 Gene-Disease associations (from GenCC):

STAT3-related early-onset multisystem autoimmune disease
Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ADIPOQ links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_004797.4, 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 ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 points.

GnomAD effective popmax AF >1% — B1 stand-alone benign; GnomAD effective popmax AF = 0.869 — exceeds 1% threshold (B1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_004797.4. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOQ	NM_004797.4	MANE Select	c.-8-3963G>A		intron	N/A	NP_004788.1	Q15848
	ADIPOQ	NM_001177800.2		c.-9+3481G>A		intron	N/A	NP_001171271.1	A8K660

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADIPOQ	ENST00000320741.7	TSL:1 MANE Select	c.-8-3963G>A	intron	N/A	ENSP00000320709.2	Q15848
ADIPOQ	ENST00000444204.2	TSL:1	c.-9+3481G>A	intron	N/A	ENSP00000389814.2	Q15848
ADIPOQ	ENST00000881747.1		c.-9+3481G>A	intron	N/A	ENSP00000551806.1

Frequencies

GnomAD3 genomes

AF:

0.813

AC:

123632

AN:

151998

Hom.:

50310

Cov.:

show subpopulations

Gnomad AFR

AF:

0.797

Gnomad AMI

AF:

0.769

Gnomad AMR

AF:

0.839

Gnomad ASJ

AF:

0.856

Gnomad EAS

AF:

0.890

Gnomad SAS

AF:

0.795

Gnomad FIN

AF:

0.819

Gnomad MID

AF:

0.842

Gnomad NFE

AF:

0.810

Gnomad OTH

AF:

0.831

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.813

AC:

123746

AN:

152116

Hom.:

50365

Cov.:

AF XY:

0.814

AC XY:

60545

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.797

AC:

33085

AN:

41490

American (AMR)

AF:

0.840

AC:

12839

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.856

AC:

2972

AN:

3472

East Asian (EAS)

AF:

0.891

AC:

4608

AN:

5172

South Asian (SAS)

AF:

0.795

AC:

3835

AN:

4824

European-Finnish (FIN)

AF:

0.819

AC:

8655

AN:

10566

Middle Eastern (MID)

AF:

0.864

AC:

254

AN:

294

European-Non Finnish (NFE)

AF:

0.810

AC:

55038

AN:

67982

Other (OTH)

AF:

0.833

AC:

1760

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1171

2341

3512

4682

5853

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

880

1760

2640

3520

4400

<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:

0.816

Hom.:

216492

Bravo

AF:

0.817

Asia WGS

AF:

0.878

AC:

3053

AN:

3478

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.950

AC:

116664

AN:

122794

Turkish Variome

AF:

0.810

AC:

1253

AN:

1546

Hom.:

506

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.876

AC:

7852

AN:

8960

Hom.:

3454

ABraOM SABE-WGS-1171

AF:

0.816

AC:

1912

AN:

2342

Hom.:

783

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.26

(source)

DANN

Benign

0.23

PhyloP100

-0.98

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

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 ACGS-UK Somatic Oncogenicity v2025

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Local populations

ClinVar

Computational scores

Splicing

Publications

Other links and lift over