chr3-186843729-A-G

Position:

• chr3-186843729-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.9).
• 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/exons	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.-9+980A>G		intron_variant		ENST00000320741.7	NP_004788.1
ADIPOQ	NM_001177800.2	c.-60+980A>G		intron_variant			NP_001171271.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.-9+980A>G		intron_variant		1	NM_004797.4	ENSP00000320709	P1
ADIPOQ	ENST00000444204.2	c.-60+980A>G		intron_variant		1		ENSP00000389814	P1

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

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.358

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

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: rs710445; hg19: chr3-186561518;