Genetic Variant ADIPOQ:c.*696C>T (chr3-186855400-C-T) – 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.*696C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 153,102 control chromosomes in the GnomAD database, including 69,602 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 0.95 ( 69015 hom., cov: 28)

Exomes 𝑓: 0.99 ( 587 hom. )

Consequence

ADIPOQ
NM_004797.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0880

Publications

24 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 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
ADIPOQ	NM_004797.4	MANE Select	c.*696C>T	3_prime_UTR	Exon 3 of 3	NP_004788.1
ADIPOQ	NM_001177800.2		c.*696C>T	3_prime_UTR	Exon 4 of 4	NP_001171271.1
ADIPOQ-AS1	NR_046662.2		n.853G>A	non_coding_transcript_exon	Exon 2 of 4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
ADIPOQ	ENST00000320741.7	TSL:1 MANE Select	c.*696C>T	3_prime_UTR	Exon 3 of 3	ENSP00000320709.2
ADIPOQ	ENST00000444204.2	TSL:1	c.*696C>T	3_prime_UTR	Exon 4 of 4	ENSP00000389814.2
ADIPOQ	ENST00000881747.1		c.*696C>T	3_prime_UTR	Exon 3 of 3	ENSP00000551806.1

Frequencies

GnomAD3 genomes

AF:

0.951

AC:

144362

AN:

151798

Hom.:

68998

Cov.:

show subpopulations

Gnomad AFR

AF:

0.840

Gnomad AMI

AF:

0.999

Gnomad AMR

AF:

0.973

Gnomad ASJ

AF:

0.998

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.987

Gnomad FIN

AF:

0.999

Gnomad MID

AF:

0.984

Gnomad NFE

AF:

0.996

Gnomad OTH

AF:

0.967

GnomAD4 exome

AF:

0.995

AC:

1180

AN:

1186

Hom.:

587

Cov.:

AF XY:

0.993

AC XY:

703

AN XY:

708

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.972

AC:

105

AN:

108

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.958

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.999

AC:

987

AN:

988

Other (OTH)

AF:

0.964

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.433

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.951

AC:

144422

AN:

151916

Hom.:

69015

Cov.:

AF XY:

0.952

AC XY:

70620

AN XY:

74178

show subpopulations

African (AFR)

AF:

0.839

AC:

34712

AN:

41356

American (AMR)

AF:

0.973

AC:

14865

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.998

AC:

3464

AN:

3472

East Asian (EAS)

AF:

1.00

AC:

5152

AN:

5152

South Asian (SAS)

AF:

0.988

AC:

4751

AN:

4810

European-Finnish (FIN)

AF:

0.999

AC:

10505

AN:

10516

Middle Eastern (MID)

AF:

0.983

AC:

289

AN:

294

European-Non Finnish (NFE)

AF:

0.996

AC:

67734

AN:

68022

Other (OTH)

AF:

0.967

AC:

2039

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

320

640

961

1281

1601

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

910

1820

2730

3640

4550

<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:

0.975

Hom.:

77178

Bravo

AF:

0.944

Asia WGS

AF:

0.980

AC:

3406

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.9

(source)

DANN

Benign

0.47

PhyloP100

0.088

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