3-186846014-C-T

Position:

• chr3-186846014-C-T

Variant summary

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

The ENST00000320741.7(ADIPOQ):​c.-9+3265C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.85 in 152,100 control chromosomes in the GnomAD database, including 55,365 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 0.85 (55365 hom., cov: 30)
• Consequence: ADIPOQ ENST00000320741.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.-9+3265C>T		intron_variant		ENST00000320741.7	NP_004788.1
ADIPOQ	NM_001177800.2	c.-9+407C>T		intron_variant			NP_001171271.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.-9+3265C>T		intron_variant		1	NM_004797.4	ENSP00000320709	P1
ADIPOQ	ENST00000444204.2	c.-9+407C>T		intron_variant		1		ENSP00000389814	P1

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129177 AN: 151982 Hom.: 55293 Cov.: 30

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.850 AC: 129312 AN: 152100 Hom.: 55365 Cov.: 30 AF XY: 0.849 AC XY: 63108 AN XY: 74346

Gnomad4 AFR AF: 0.959

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.853

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.794

Gnomad4 OTH AF: 0.857

Alfa AF: 0.825 Hom.: 9628

Bravo AF: 0.860

Asia WGS AF: 0.885 AC: 3079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.86
DANN	Benign	0.62

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: rs822391; hg19: chr3-186563803;