chr3-186855075-C-CA

Position:

• chr3-186855075-C-CA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_004797.4(ADIPOQ):​c.*372dupA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.55 (23416 hom., cov: 0)
  • Exomes 𝑓: 0.58 (31248 hom.)
• Consequence: ADIPOQ NM_004797.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.*372dupA		3_prime_UTR_variant	3/3	ENST00000320741.7	NP_004788.1
ADIPOQ	NM_001177800.2	c.*372dupA		3_prime_UTR_variant	4/4		NP_001171271.1
ADIPOQ-AS1	NR_046662.2	n.1177dupT		non_coding_transcript_exon_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.*372dupA		3_prime_UTR_variant	3/3	1	NM_004797.4	ENSP00000320709.2
ADIPOQ	ENST00000444204.2	c.*372dupA		3_prime_UTR_variant	4/4	1		ENSP00000389814.2
ADIPOQ-AS1	ENST00000422718.1	n.1048dupT		non_coding_transcript_exon_variant	1/3	5

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83239 AN: 151818 Hom.: 23402 Cov.: 0

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.512

GnomAD4 exome AF: 0.583 AC: 103881 AN: 178140 Hom.: 31248 Cov.: 0 AF XY: 0.586 AC XY: 56930 AN XY: 97084

Gnomad4 AFR exome AF: 0.407

Gnomad4 AMR exome AF: 0.484

Gnomad4 ASJ exome AF: 0.475

Gnomad4 EAS exome AF: 0.402

Gnomad4 SAS exome AF: 0.630

Gnomad4 FIN exome AF: 0.624

Gnomad4 NFE exome AF: 0.600

Gnomad4 OTH exome AF: 0.571

GnomAD4 genome AF: 0.548 AC: 83275 AN: 151936 Hom.: 23416 Cov.: 0 AF XY: 0.548 AC XY: 40682 AN XY: 74278

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.512

Alfa AF: 0.593 Hom.: 3279

Bravo AF: 0.532

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs56354395; hg19: chr3-186572864;