rs4686804

Positions:

• chr3-186856697-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.*1993G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,804 control chromosomes in the GnomAD database, including 19,669 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 0.50 (19669 hom., cov: 31)
  • Exomes 𝑓: 0.58 (3 hom.)
  • Failed GnomAD Quality Control
• Consequence: ADIPOQ NM_004797.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.*1993G>A		3_prime_UTR_variant	3/3	ENST00000320741.7	NP_004788.1
ADIPOQ-AS1	NR_046662.2	n.137-581C>T		intron_variant, non_coding_transcript_variant
ADIPOQ	NM_001177800.2	c.*1993G>A		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.*1993G>A		3_prime_UTR_variant	3/3	1	NM_004797.4	ENSP00000320709	P1
ADIPOQ	ENST00000444204.2	c.*1993G>A		3_prime_UTR_variant	4/4	1		ENSP00000389814	P1

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76492 AN: 151682 Hom.: 19657 Cov.: 31

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.472

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.583 AC: 7 AN: 12 Hom.: 3 Cov.: 0 AF XY: 0.750 AC XY: 6 AN XY: 8

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.625

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.504 AC: 76527 AN: 151804 Hom.: 19669 Cov.: 31 AF XY: 0.502 AC XY: 37229 AN XY: 74198

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.471

Alfa AF: 0.543 Hom.: 2852

Bravo AF: 0.497

Asia WGS AF: 0.443 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.41
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: rs4686804; hg19: chr3-186574486;