rs710445

Variant names:

• chr3-186843729-A-G
• rs710445
• NM_004797.4:c.-9+980A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-186843729-A-G
• chr3-186843729-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.-9+980A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 150,456 control chromosomes in the GnomAD database, including 12,117 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 0.39 (12117 hom., cov: 28)
• Consequence: ADIPOQ NM_004797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.-9+980A>G		intron_variant	Intron 1 of 2	ENST00000320741.7	NP_004788.1
ADIPOQ	NM_001177800.2	c.-60+980A>G		intron_variant	Intron 1 of 3		NP_001171271.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.-9+980A>G		intron_variant	Intron 1 of 2	1	NM_004797.4	ENSP00000320709.2
ADIPOQ	ENST00000444204.2	c.-60+980A>G		intron_variant	Intron 1 of 3	1		ENSP00000389814.2

Frequencies

GnomAD3 genomes AF: 0.391 AC: 58828 AN: 150340 Hom.: 12103 Cov.: 28

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.391 AC: 58881 AN: 150456 Hom.: 12117 Cov.: 28 AF XY: 0.401 AC XY: 29355 AN XY: 73266

African (AFR) AF: 0.389 AC: 15913 AN: 40942

American (AMR) AF: 0.424 AC: 6391 AN: 15084

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1273 AN: 3470

East Asian (EAS) AF: 0.475 AC: 2426 AN: 5108

South Asian (SAS) AF: 0.347 AC: 1668 AN: 4800

European-Finnish (FIN) AF: 0.596 AC: 5898 AN: 9900

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.353 AC: 23933 AN: 67840

Other (OTH) AF: 0.358 AC: 754 AN: 2108

Alfa AF: 0.247 Hom.: 623

Bravo AF: 0.383

Asia WGS AF: 0.444 AC: 1543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.77
DANN	Benign	0.67
PhyloP100		-0.13
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: rs710445; hg19: chr3-186561518;