rs9882205

Variant names:

• chr3-186852609-G-A
• rs9882205
• NM_004797.4:c.-8-442G>A

Variant summary

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

The NM_004797.4(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 NM_004797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 6 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOQ	NM_004797.4	MANE Select	c.-8-442G>A		intron	N/A	NP_004788.1	Q15848
	ADIPOQ	NM_001177800.2		c.-8-442G>A		intron	N/A	NP_001171271.1	A8K660
	ADIPOQ-AS1	NR_046662.2		n.2849C>T		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOQ	ENST00000320741.7	TSL:1 MANE Select	c.-8-442G>A		intron	N/A	ENSP00000320709.2	Q15848
	ADIPOQ	ENST00000444204.2	TSL:1	c.-8-442G>A		intron	N/A	ENSP00000389814.2	Q15848
	ADIPOQ	ENST00000956685.1		c.-450G>A		5_prime_UTR	Exon 1 of 2	ENSP00000626744.1

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

African (AFR) AF: 0.183 AC: 143 AN: 782

American (AMR) AF: 0.249 AC: 793 AN: 3182

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 163 AN: 632

East Asian (EAS) AF: 0.512 AC: 899 AN: 1756

South Asian (SAS) AF: 0.404 AC: 868 AN: 2148

European-Finnish (FIN) AF: 0.212 AC: 442 AN: 2080

Middle Eastern (MID) AF: 0.349 AC: 30 AN: 86

European-Non Finnish (NFE) AF: 0.241 AC: 4670 AN: 19342

Other (OTH) AF: 0.254 AC: 424 AN: 1668

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

African (AFR) AF: 0.229 AC: 9503 AN: 41472

American (AMR) AF: 0.300 AC: 4575 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3468

East Asian (EAS) AF: 0.595 AC: 3058 AN: 5142

South Asian (SAS) AF: 0.460 AC: 2213 AN: 4814

European-Finnish (FIN) AF: 0.259 AC: 2744 AN: 10576

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19055 AN: 67992

Other (OTH) AF: 0.334 AC: 704 AN: 2110

Alfa AF: 0.284 Hom.: 9707

Bravo AF: 0.281

Asia WGS AF: 0.512 AC: 1780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.054
DANN	Benign	0.41
PhyloP100		-1.2
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9882205;

hg19: chr3-186570398;