dbSNP rs3821799: ADIPOQ:c.214+425T>C (chr3-186853697-T-C) – 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.214+425T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 224,586 control chromosomes in the GnomAD database, including 30,041 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 0.50 ( 19696 hom., cov: 31)

Exomes 𝑓: 0.53 ( 10345 hom. )

Consequence

ADIPOQ
NM_004797.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.107

Publications

55 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=-0.81).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
ADIPOQ	NM_004797.4 link	c.214+425T>C	intron_variant	Intron 2 of 2	ENST00000320741.7	NP_004788.1	Q15848A8K660
ADIPOQ	NM_001177800.2 link	c.214+425T>C	intron_variant	Intron 3 of 3		NP_001171271.1	Q15848A8K660B2R773
ADIPOQ-AS1	NR_046662.2 link	n.2215+81A>G	intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ADIPOQ	ENST00000320741.7 link	c.214+425T>C	intron_variant	Intron 2 of 2	1	NM_004797.4	ENSP00000320709.2	Q15848
ADIPOQ	ENST00000444204.2 link	c.214+425T>C	intron_variant	Intron 3 of 3	1		ENSP00000389814.2	Q15848
ADIPOQ-AS1	ENST00000422718.1 link	n.2086+81A>G	intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.504

AC:

76540

AN:

151776

Hom.:

19683

Cov.:

show subpopulations

Gnomad AFR

AF:

0.425

Gnomad AMI

AF:

0.591

Gnomad AMR

AF:

0.460

Gnomad ASJ

AF:

0.470

Gnomad EAS

AF:

0.395

Gnomad SAS

AF:

0.559

Gnomad FIN

AF:

0.556

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.561

Gnomad OTH

AF:

0.470

GnomAD4 exome

AF:

0.526

AC:

38209

AN:

72692

Hom.:

10345

AF XY:

0.526

AC XY:

19835

AN XY:

37686

show subpopulations

African (AFR)

AF:

0.400

AC:

829

AN:

2070

American (AMR)

AF:

0.515

AC:

2129

AN:

4136

Ashkenazi Jewish (ASJ)

AF:

0.436

AC:

838

AN:

1922

East Asian (EAS)

AF:

0.385

AC:

1502

AN:

3900

South Asian (SAS)

AF:

0.557

AC:

4408

AN:

7910

European-Finnish (FIN)

AF:

0.530

AC:

1758

AN:

3318

Middle Eastern (MID)

AF:

0.443

AC:

117

AN:

264

European-Non Finnish (NFE)

AF:

0.545

AC:

24646

AN:

45248

Other (OTH)

AF:

0.505

AC:

1982

AN:

3924

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

860

1720

2579

3439

4299

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

248

496

744

992

1240

<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:

0.504

AC:

76575

AN:

151894

Hom.:

19696

Cov.:

AF XY:

0.501

AC XY:

37215

AN XY:

74212

show subpopulations

African (AFR)

AF:

0.424

AC:

17567

AN:

41420

American (AMR)

AF:

0.460

AC:

7008

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.470

AC:

1629

AN:

3468

East Asian (EAS)

AF:

0.395

AC:

2035

AN:

5150

South Asian (SAS)

AF:

0.562

AC:

2704

AN:

4810

European-Finnish (FIN)

AF:

0.556

AC:

5846

AN:

10520

Middle Eastern (MID)

AF:

0.415

AC:

122

AN:

294

European-Non Finnish (NFE)

AF:

0.561

AC:

38139

AN:

67970

Other (OTH)

AF:

0.468

AC:

986

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1920

3840

5760

7680

9600

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

704

1408

2112

2816

3520

<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:

0.533

Hom.:

89400

Bravo

AF:

0.497

Asia WGS

AF:

0.442

AC:

1536

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

9.1

(source)

DANN

Benign

0.84

PhyloP100

-0.11

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