rs9882205

Positions:

• chr3-186852609-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000320741.7(ADIPOQ):​c.-8-442G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 183,710 control chromosomes in the GnomAD database, including 7,915 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 0.29 (6624 hom., cov: 32)
  • Exomes 𝑓: 0.27 (1291 hom.)
• Consequence: ADIPOQ ENST00000320741.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.-8-442G>A		intron_variant		ENST00000320741.7	NP_004788.1
ADIPOQ-AS1	NR_046662.2	n.2849C>T		non_coding_transcript_exon_variant	4/4
ADIPOQ	NM_001177800.2	c.-8-442G>A		intron_variant			NP_001171271.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.-8-442G>A		intron_variant		1	NM_004797.4	ENSP00000320709	P1
ADIPOQ	ENST00000444204.2	c.-8-442G>A		intron_variant		1		ENSP00000389814	P1
ADIPOQ-AS1	ENST00000422718.1	n.2720C>T		non_coding_transcript_exon_variant	3/3	5

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43281 AN: 151916 Hom.: 6619 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.329

GnomAD4 exome AF: 0.266 AC: 8432 AN: 31676 Hom.: 1291 Cov.: 0 AF XY: 0.275 AC XY: 4497 AN XY: 16376

Gnomad4 AFR exome AF: 0.183

Gnomad4 AMR exome AF: 0.249

Gnomad4 ASJ exome AF: 0.258

Gnomad4 EAS exome AF: 0.512

Gnomad4 SAS exome AF: 0.404

Gnomad4 FIN exome AF: 0.212

Gnomad4 NFE exome AF: 0.241

Gnomad4 OTH exome AF: 0.254

GnomAD4 genome AF: 0.285 AC: 43334 AN: 152034 Hom.: 6624 Cov.: 32 AF XY: 0.292 AC XY: 21721 AN XY: 74298

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.595

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.334

Alfa AF: 0.172 Hom.: 371

Bravo AF: 0.281

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.054
DANN	Benign	0.41

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: rs9882205; hg19: chr3-186570398;