3-186852664-G-A

Position:

• chr3-186852664-G-A

Variant summary

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

The NM_004797.4(ADIPOQ):​c.-8-387G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0912 in 219,184 control chromosomes in the GnomAD database, including 1,200 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 0.088 (819 hom., cov: 32)
  • Exomes 𝑓: 0.098 (381 hom.)
• Consequence: ADIPOQ NM_004797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

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-AS1 (HGNC:40648): (ADIPOQ antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADIPOQ	NM_004797.4	c.-8-387G>A		intron_variant		ENST00000320741.7
ADIPOQ-AS1	NR_046662.2	n.2794C>T		non_coding_transcript_exon_variant	4/4
ADIPOQ	NM_001177800.2	c.-8-387G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.-8-387G>A		intron_variant		1	NM_004797.4	P1
ADIPOQ	ENST00000444204.2	c.-8-387G>A		intron_variant		1		P1
ADIPOQ-AS1	ENST00000422718.1	n.2665C>T		non_coding_transcript_exon_variant	3/3	5

Frequencies

GnomAD3 genomes AF: 0.0882 AC: 13427 AN: 152158 Hom.: 820 Cov.: 32

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.0690

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.0971

GnomAD4 exome AF: 0.0979 AC: 6553 AN: 66908 Hom.: 381 Cov.: 0 AF XY: 0.100 AC XY: 3489 AN XY: 34798

Gnomad4 AFR exome AF: 0.0199

Gnomad4 AMR exome AF: 0.0596

Gnomad4 ASJ exome AF: 0.121

Gnomad4 EAS exome AF: 0.0241

Gnomad4 SAS exome AF: 0.117

Gnomad4 FIN exome AF: 0.130

Gnomad4 NFE exome AF: 0.108

Gnomad4 OTH exome AF: 0.0998

GnomAD4 genome AF: 0.0882 AC: 13427 AN: 152276 Hom.: 819 Cov.: 32 AF XY: 0.0903 AC XY: 6719 AN XY: 74446

Gnomad4 AFR AF: 0.0210

Gnomad4 AMR AF: 0.0689

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0297

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.0975

Alfa AF: 0.117 Hom.: 1510

Bravo AF: 0.0792

Asia WGS AF: 0.0710 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.4
DANN	Benign	0.61

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: rs17366568; hg19: chr3-186570453;