Genetic Variant ADIPOQ:c.*1212A>G (chr3-186855916-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.*1212A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 152,116 control chromosomes in the GnomAD database, including 23,451 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 ( 23441 hom., cov: 32)

Exomes 𝑓: 0.63 ( 10 hom. )

Consequence

ADIPOQ
NM_004797.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.321

Publications

82 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=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.627 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.*1212A>G	3_prime_UTR	Exon 3 of 3	NP_004788.1	Q15848
ADIPOQ	NM_001177800.2		c.*1212A>G	3_prime_UTR	Exon 4 of 4	NP_001171271.1	A8K660
ADIPOQ-AS1	NR_046662.2		n.337T>C	non_coding_transcript_exon	Exon 2 of 4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADIPOQ	ENST00000320741.7	TSL:1 MANE Select	c.*1212A>G	3_prime_UTR	Exon 3 of 3	ENSP00000320709.2	Q15848
ADIPOQ	ENST00000444204.2	TSL:1	c.*1212A>G	3_prime_UTR	Exon 4 of 4	ENSP00000389814.2	Q15848
ADIPOQ	ENST00000881747.1		c.*1212A>G	3_prime_UTR	Exon 3 of 3	ENSP00000551806.1

Frequencies

GnomAD3 genomes

AF:

0.548

AC:

83286

AN:

151942

Hom.:

23428

Cov.:

show subpopulations

Gnomad AFR

AF:

0.435

Gnomad AMI

AF:

0.670

Gnomad AMR

AF:

0.490

Gnomad ASJ

AF:

0.500

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.644

Gnomad FIN

AF:

0.645

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.620

Gnomad OTH

AF:

0.511

GnomAD4 exome

AF:

0.625

AC:

AN:

Hom.:

Cov.:

AF XY:

0.600

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

0.700

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.625

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.594

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<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:

83319

AN:

152060

Hom.:

23441

Cov.:

AF XY:

0.547

AC XY:

40682

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.434

AC:

18008

AN:

41478

American (AMR)

AF:

0.490

AC:

7492

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

1732

AN:

3466

East Asian (EAS)

AF:

0.424

AC:

2188

AN:

5164

South Asian (SAS)

AF:

0.646

AC:

3114

AN:

4824

European-Finnish (FIN)

AF:

0.645

AC:

6812

AN:

10568

Middle Eastern (MID)

AF:

0.459

AC:

135

AN:

294

European-Non Finnish (NFE)

AF:

0.620

AC:

42148

AN:

67960

Other (OTH)

AF:

0.511

AC:

1080

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1929

3858

5786

7715

9644

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

738

1476

2214

2952

3690

<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:

0.581

Hom.:

76230

Bravo

AF:

0.534

Asia WGS

AF:

0.495

AC:

1723

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.8

(source)

DANN

Benign

0.38

PhyloP100

0.32

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