rs3821799

Positions:

• chr3-186853697-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.214+425T>C		intron_variant		ENST00000320741.7	NP_004788.1
ADIPOQ-AS1	NR_046662.2	n.2215+81A>G		intron_variant, non_coding_transcript_variant
ADIPOQ	NM_001177800.2	c.214+425T>C		intron_variant			NP_001171271.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.214+425T>C		intron_variant		1	NM_004797.4	ENSP00000320709	P1
ADIPOQ	ENST00000444204.2	c.214+425T>C		intron_variant		1		ENSP00000389814	P1
ADIPOQ-AS1	ENST00000422718.1	n.2086+81A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR exome AF: 0.400

Gnomad4 AMR exome AF: 0.515

Gnomad4 ASJ exome AF: 0.436

Gnomad4 EAS exome AF: 0.385

Gnomad4 SAS exome AF: 0.557

Gnomad4 FIN exome AF: 0.530

Gnomad4 NFE exome AF: 0.545

Gnomad4 OTH exome AF: 0.505

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

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.395

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.468

Alfa AF: 0.539 Hom.: 43491

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
DANN	Benign	0.84

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

LitVar

Other links and lift over

dbSNP: rs3821799; hg19: chr3-186571486;