chr3-186856300-G-T

Position:

• chr3-186856300-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.*1596G>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 0.00445 in 152,248 control chromosomes in the GnomAD database, including 8 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 0.0044 (8 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ADIPOQ NM_004797.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.*1596G>T		3_prime_UTR_variant	3/3	ENST00000320741.7	NP_004788.1
ADIPOQ	NM_001177800.2	c.*1596G>T		3_prime_UTR_variant	4/4		NP_001171271.1
ADIPOQ-AS1	NR_046662.2	n.137-184C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.*1596G>T		3_prime_UTR_variant	3/3	1	NM_004797.4	ENSP00000320709.2
ADIPOQ	ENST00000444204.2	c.*1596G>T		3_prime_UTR_variant	4/4	1		ENSP00000389814.2

Frequencies

GnomAD3 genomes AF: 0.00445 AC: 677 AN: 152130 Hom.: 8 Cov.: 33

Gnomad AFR AF: 0.000676

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000786

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0554

Gnomad SAS AF: 0.00332

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000750

Gnomad OTH AF: 0.00144

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

GnomAD4 genome AF: 0.00445 AC: 677 AN: 152248 Hom.: 8 Cov.: 33 AF XY: 0.00561 AC XY: 418 AN XY: 74468

Gnomad4 AFR AF: 0.000674

Gnomad4 AMR AF: 0.000785

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0555

Gnomad4 SAS AF: 0.00332

Gnomad4 FIN AF: 0.0262

Gnomad4 NFE AF: 0.000750

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.00296 Hom.: 0

Bravo AF: 0.00246

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.1
DANN	Benign	0.74

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: rs17846872; hg19: chr3-186574089;