Genetic Variant NM_004797.4:c.214+62G>T (chr3-186853334-G-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.214+62G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 1,524,528 control chromosomes in the GnomAD database, including 56,885 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 0.30 ( 6968 hom., cov: 33)

Exomes 𝑓: 0.27 ( 49917 hom. )

Consequence

ADIPOQ
NM_004797.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.683

Publications

683 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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
ADIPOQ	NM_004797.4 link	c.214+62G>T	intron_variant	Intron 2 of 2	ENST00000320741.7	NP_004788.1
ADIPOQ	NM_001177800.2 link	c.214+62G>T	intron_variant	Intron 3 of 3		NP_001171271.1
ADIPOQ-AS1	NR_046662.2 link	n.2216-92C>A	intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
ADIPOQ	ENST00000320741.7 link	c.214+62G>T	intron_variant	Intron 2 of 2	1	NM_004797.4	ENSP00000320709.2
ADIPOQ	ENST00000444204.2 link	c.214+62G>T	intron_variant	Intron 3 of 3	1		ENSP00000389814.2
ADIPOQ-AS1	ENST00000422718.1 link	n.2087-92C>A	intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.301

AC:

45832

AN:

152038

Hom.:

6963

Cov.:

show subpopulations

Gnomad AFR

AF:

0.360

Gnomad AMI

AF:

0.255

Gnomad AMR

AF:

0.310

Gnomad ASJ

AF:

0.298

Gnomad EAS

AF:

0.284

Gnomad SAS

AF:

0.220

Gnomad FIN

AF:

0.312

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.270

Gnomad OTH

AF:

0.300

GnomAD4 exome

AF:

0.267

AC:

366658

AN:

1372372

Hom.:

49917

AF XY:

0.265

AC XY:

180130

AN XY:

678606

show subpopulations

African (AFR)

AF:

0.365

AC:

11334

AN:

31076

American (AMR)

AF:

0.278

AC:

9906

AN:

35666

Ashkenazi Jewish (ASJ)

AF:

0.314

AC:

7873

AN:

25036

East Asian (EAS)

AF:

0.282

AC:

10038

AN:

35636

South Asian (SAS)

AF:

0.226

AC:

17668

AN:

78338

European-Finnish (FIN)

AF:

0.310

AC:

15262

AN:

49294

Middle Eastern (MID)

AF:

0.306

AC:

1630

AN:

5324

European-Non Finnish (NFE)

AF:

0.263

AC:

277317

AN:

1054976

Other (OTH)

AF:

0.274

AC:

15630

AN:

57026

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

13511

27023

40534

54046

67557

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9292

18584

27876

37168

46460

<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:

0.301

AC:

45857

AN:

152156

Hom.:

6968

Cov.:

AF XY:

0.301

AC XY:

22388

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.360

AC:

14930

AN:

41510

American (AMR)

AF:

0.310

AC:

4740

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.298

AC:

1032

AN:

3466

East Asian (EAS)

AF:

0.284

AC:

1469

AN:

5168

South Asian (SAS)

AF:

0.219

AC:

1058

AN:

4822

European-Finnish (FIN)

AF:

0.312

AC:

3310

AN:

10596

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.270

AC:

18369

AN:

67980

Other (OTH)

AF:

0.299

AC:

633

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1701

3401

5102

6802

8503

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

450

900

1350

1800

2250

<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:

0.278

Hom.:

22656

Bravo

AF:

0.302

Asia WGS

AF:

0.281

AC:

978

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.57

(source)

DANN

Benign

0.48

PhyloP100

-0.68

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