rs822394

Positions:

• chr3-186848939-A-C
• chr3-186848939-A-G
• chr3-186848939-A-T

Variant summary

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

The NM_004797.4(ADIPOQ):​c.-8-4112A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,136 control chromosomes in the GnomAD database, including 56,711 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 0.86 (56711 hom., cov: 31)
• Consequence: ADIPOQ NM_004797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADIPOQ	NM_004797.4	c.-8-4112A>C		intron_variant		ENST00000320741.7
ADIPOQ	NM_001177800.2	c.-9+3332A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.-8-4112A>C		intron_variant		1	NM_004797.4	P1
ADIPOQ	ENST00000444204.2	c.-9+3332A>C		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130831 AN: 152018 Hom.: 56640 Cov.: 31

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.861 AC: 130965 AN: 152136 Hom.: 56711 Cov.: 31 AF XY: 0.860 AC XY: 63928 AN XY: 74354

Gnomad4 AFR AF: 0.962

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.860

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.863

Alfa AF: 0.820 Hom.: 63569

Bravo AF: 0.869

Asia WGS AF: 0.889 AC: 3093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.39

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: rs822394; hg19: chr3-186566728;