Genetic Variant ADIPOQ:c.215-414A>G (chr3-186853770-A-G) – 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.215-414A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 219,150 control chromosomes in the GnomAD database, including 35,445 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 0.55 ( 23347 hom., cov: 29)

Exomes 𝑓: 0.59 ( 12098 hom. )

Consequence

ADIPOQ
NM_004797.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00700

Publications

99 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:

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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 (SAS) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Variant Effect in Transcripts

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

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADIPOQ	NM_004797.4	MANE Select	c.215-414A>G	intron	N/A	NP_004788.1	Q15848
ADIPOQ	NM_001177800.2		c.215-414A>G	intron	N/A	NP_001171271.1	A8K660
ADIPOQ-AS1	NR_046662.2		n.2215+8T>C	splice_region intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADIPOQ	ENST00000320741.7	TSL:1 MANE Select	c.215-414A>G	intron	N/A	ENSP00000320709.2	Q15848
ADIPOQ	ENST00000444204.2	TSL:1	c.215-414A>G	intron	N/A	ENSP00000389814.2	Q15848
ADIPOQ	ENST00000881747.1		c.215-414A>G	intron	N/A	ENSP00000551806.1

Frequencies

GnomAD3 genomes

AF:

0.548

AC:

82958

AN:

151318

Hom.:

23333

Cov.:

show subpopulations

Gnomad AFR

AF:

0.435

Gnomad AMI

AF:

0.671

Gnomad AMR

AF:

0.490

Gnomad ASJ

AF:

0.500

Gnomad EAS

AF:

0.425

Gnomad SAS

AF:

0.643

Gnomad FIN

AF:

0.643

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.620

Gnomad OTH

AF:

0.511

GnomAD4 exome

AF:

0.586

AC:

39679

AN:

67714

Hom.:

12098

Cov.:

AF XY:

0.586

AC XY:

20350

AN XY:

34714

show subpopulations

African (AFR)

AF:

0.415

AC:

822

AN:

1982

American (AMR)

AF:

0.534

AC:

2274

AN:

4262

Ashkenazi Jewish (ASJ)

AF:

0.472

AC:

891

AN:

1886

East Asian (EAS)

AF:

0.404

AC:

1682

AN:

4164

South Asian (SAS)

AF:

0.644

AC:

3841

AN:

5960

European-Finnish (FIN)

AF:

0.626

AC:

1891

AN:

3022

Middle Eastern (MID)

AF:

0.461

AC:

119

AN:

258

European-Non Finnish (NFE)

AF:

0.613

AC:

25983

AN:

42376

Other (OTH)

AF:

0.572

AC:

2176

AN:

3804

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

771

1542

2314

3085

3856

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

256

512

768

1024

1280

<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:

0.548

AC:

82994

AN:

151436

Hom.:

23347

Cov.:

AF XY:

0.548

AC XY:

40476

AN XY:

73924

show subpopulations

African (AFR)

AF:

0.434

AC:

17900

AN:

41212

American (AMR)

AF:

0.490

AC:

7447

AN:

15188

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

1734

AN:

3466

East Asian (EAS)

AF:

0.424

AC:

2184

AN:

5146

South Asian (SAS)

AF:

0.645

AC:

3088

AN:

4784

European-Finnish (FIN)

AF:

0.643

AC:

6729

AN:

10458

Middle Eastern (MID)

AF:

0.459

AC:

135

AN:

294

European-Non Finnish (NFE)

AF:

0.620

AC:

42092

AN:

67876

Other (OTH)

AF:

0.511

AC:

1073

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1841

3682

5524

7365

9206

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

736

1472

2208

2944

3680

<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:

0.592

Hom.:

37848

Bravo

AF:

0.534

Asia WGS

AF:

0.495

AC:

1721

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.57

(source)

DANN

Benign

0.52

PhyloP100

0.0070

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over