rs1063537

Positions:

• chr3-186856286-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.*1582C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,204 control chromosomes in the GnomAD database, including 1,077 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 0.10 (1077 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ADIPOQ NM_004797.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.*1582C>T		3_prime_UTR_variant	3/3	ENST00000320741.7	NP_004788.1
ADIPOQ	NM_001177800.2	c.*1582C>T		3_prime_UTR_variant	4/4		NP_001171271.1
ADIPOQ-AS1	NR_046662.2	n.137-170G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.*1582C>T		3_prime_UTR_variant	3/3	1	NM_004797.4	ENSP00000320709.2
ADIPOQ	ENST00000444204.2	c.*1582C>T		3_prime_UTR_variant	4/4	1		ENSP00000389814.2

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15297 AN: 152086 Hom.: 1079 Cov.: 33

Gnomad AFR AF: 0.0328

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0435

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.155

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.101 AC: 15301 AN: 152204 Hom.: 1077 Cov.: 33 AF XY: 0.103 AC XY: 7667 AN XY: 74412

Gnomad4 AFR AF: 0.0328

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0435

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.159

Alfa AF: 0.123 Hom.: 1231

Bravo AF: 0.108

Asia WGS AF: 0.206 AC: 716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.45
DANN	Benign	0.40

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: rs1063537; hg19: chr3-186574075;