rs822394

Variant names:

• chr3-186848939-A-C
• rs822394
• NM_004797.4:c.-8-4112A>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_004797.4(ADIPOQ):​c.-8-4112A>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
• Publications: 26 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 Gene-Disease associations (from GenCC):

• STAT3-related early-onset multisystem autoimmune disease

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.-8-4112A>C		intron_variant	Intron 1 of 2	ENST00000320741.7	NP_004788.1
ADIPOQ	NM_001177800.2	c.-9+3332A>C		intron_variant	Intron 2 of 3		NP_001171271.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.-8-4112A>C		intron_variant	Intron 1 of 2	1	NM_004797.4	ENSP00000320709.2
ADIPOQ	ENST00000444204.2	c.-9+3332A>C		intron_variant	Intron 2 of 3	1		ENSP00000389814.2

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

African (AFR) AF: 0.962 AC: 39946 AN: 41528

American (AMR) AF: 0.858 AC: 13098 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2986 AN: 3472

East Asian (EAS) AF: 0.889 AC: 4593 AN: 5168

South Asian (SAS) AF: 0.795 AC: 3835 AN: 4822

European-Finnish (FIN) AF: 0.819 AC: 8650 AN: 10566

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55078 AN: 67996

Other (OTH) AF: 0.863 AC: 1820 AN: 2108

Alfa AF: 0.826 Hom.: 83377

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
PhyloP100		-2.2
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

Other links and lift over

dbSNP: rs822394; hg19: chr3-186566728;