rs62292784

chr3-186843108-C-T

Variant summary

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

The NM_004797.4(ADIPOQ):c.-9+359C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,082 control chromosomes in the GnomAD database, including 4,340 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 0.23 (4340 hom., cov: 32)
• Consequence: ADIPOQ NM_004797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.149

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADIPOQ	NM_004797.4	c.-9+359C>T		intron_variant		ENST00000320741.7
ADIPOQ	NM_001177800.2	c.-60+359C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.-9+359C>T		intron_variant		1	NM_004797.4	P1
ADIPOQ	ENST00000444204.2	c.-60+359C>T		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34242 AN: 151964 Hom.: 4340 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.225 AC: 34254 AN: 152082 Hom.: 4340 Cov.: 32 AF XY: 0.228 AC XY: 16974 AN XY: 74354

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.217

Alfa AF: 0.252 Hom.: 1229

Bravo AF: 0.219

Asia WGS AF: 0.268 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.7
Dann	Benign	0.54

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: rs62292784; hg19: chr3-186560897;