rs822395

Positions:

• chr3-186849018-C-A
• chr3-186849018-C-G

Variant summary

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

The NM_004797.4(ADIPOQ):​c.-8-4033C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 151,928 control chromosomes in the GnomAD database, including 32,601 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 0.65 (32601 hom., cov: 31)
• Consequence: ADIPOQ NM_004797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADIPOQ	NM_004797.4	c.-8-4033C>A		intron_variant		ENST00000320741.7
ADIPOQ	NM_001177800.2	c.-9+3411C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.-8-4033C>A		intron_variant		1	NM_004797.4	P1
ADIPOQ	ENST00000444204.2	c.-9+3411C>A		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.652 AC: 98932 AN: 151810 Hom.: 32567 Cov.: 31

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.654

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.652 AC: 99010 AN: 151928 Hom.: 32601 Cov.: 31 AF XY: 0.655 AC XY: 48649 AN XY: 74238

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.657

Alfa AF: 0.622 Hom.: 7925

Bravo AF: 0.649

Asia WGS AF: 0.788 AC: 2735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.8
DANN	Benign	0.78

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: rs822395; hg19: chr3-186566807;