3-186853697-T-C

Variant names:

• chr3-186853697-T-C
• rs3821799
• NM_004797.4:c.214+425T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 55 publications found

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-AS1 (HGNC:40648): (ADIPOQ antisense RNA 1)

ACMG classification

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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOQ	NM_004797.4	MANE Select	c.214+425T>C		intron	N/A	NP_004788.1
	ADIPOQ	NM_001177800.2		c.214+425T>C		intron	N/A	NP_001171271.1
	ADIPOQ-AS1	NR_046662.2		n.2215+81A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOQ	ENST00000320741.7	TSL:1 MANE Select	c.214+425T>C		intron	N/A	ENSP00000320709.2
	ADIPOQ	ENST00000444204.2	TSL:1	c.214+425T>C		intron	N/A	ENSP00000389814.2
	ADIPOQ-AS1	ENST00000422718.1	TSL:5	n.2086+81A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76540 AN: 151776 Hom.: 19683 Cov.: 31

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

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

GnomAD4 genome AF: 0.504 AC: 76575 AN: 151894 Hom.: 19696 Cov.: 31 AF XY: 0.501 AC XY: 37215 AN XY: 74212

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.1
DANN	Benign	0.84
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3821799; hg19: chr3-186571486;