3-186853334-G-T

Position:

• chr3-186853334-G-T

Variant summary

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

The NM_004797.4(ADIPOQ):​c.214+62G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 1,524,528 control chromosomes in the GnomAD database, including 56,885 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 0.30 (6968 hom., cov: 33)
  • Exomes 𝑓: 0.27 (49917 hom.)
• Consequence: ADIPOQ NM_004797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.214+62G>T		intron_variant		ENST00000320741.7	NP_004788.1
ADIPOQ	NM_001177800.2	c.214+62G>T		intron_variant			NP_001171271.1
ADIPOQ-AS1	NR_046662.2	n.2216-92C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.214+62G>T		intron_variant		1	NM_004797.4	ENSP00000320709.2
ADIPOQ	ENST00000444204.2	c.214+62G>T		intron_variant		1		ENSP00000389814.2
ADIPOQ-AS1	ENST00000422718.1	n.2087-92C>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45832 AN: 152038 Hom.: 6963 Cov.: 33

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.300

GnomAD4 exome AF: 0.267 AC: 366658 AN: 1372372 Hom.: 49917 AF XY: 0.265 AC XY: 180130 AN XY: 678606

Gnomad4 AFR exome AF: 0.365

Gnomad4 AMR exome AF: 0.278

Gnomad4 ASJ exome AF: 0.314

Gnomad4 EAS exome AF: 0.282

Gnomad4 SAS exome AF: 0.226

Gnomad4 FIN exome AF: 0.310

Gnomad4 NFE exome AF: 0.263

Gnomad4 OTH exome AF: 0.274

GnomAD4 genome AF: 0.301 AC: 45857 AN: 152156 Hom.: 6968 Cov.: 33 AF XY: 0.301 AC XY: 22388 AN XY: 74366

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.299

Alfa AF: 0.270 Hom.: 9518

Bravo AF: 0.302

Asia WGS AF: 0.281 AC: 978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.57
DANN	Benign	0.48

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: rs1501299; hg19: chr3-186571123; COSMIC: COSV57859563;