rs1063538

Positions:

• chr3-186856394-T-C

Variant summary

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

The NM_004797.4(ADIPOQ):​c.*1690T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,108 control chromosomes in the GnomAD database, including 23,399 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 0.55 (23399 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ADIPOQ NM_004797.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.*1690T>C		3_prime_UTR_variant	3/3	ENST00000320741.7	NP_004788.1
ADIPOQ-AS1	NR_046662.2	n.137-278A>G		intron_variant, non_coding_transcript_variant
ADIPOQ	NM_001177800.2	c.*1690T>C		3_prime_UTR_variant	4/4		NP_001171271.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.*1690T>C		3_prime_UTR_variant	3/3	1	NM_004797.4	ENSP00000320709	P1
ADIPOQ	ENST00000444204.2	c.*1690T>C		3_prime_UTR_variant	4/4	1		ENSP00000389814	P1

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83227 AN: 151988 Hom.: 23384 Cov.: 33

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.511

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.547 AC: 83263 AN: 152108 Hom.: 23399 Cov.: 33 AF XY: 0.547 AC XY: 40664 AN XY: 74354

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.511

Alfa AF: 0.591 Hom.: 26972

Bravo AF: 0.533

Asia WGS AF: 0.495 AC: 1721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.55

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: rs1063538; hg19: chr3-186574183;