chr3-186855075-C-CA

Variant names:

• chr3-186855075-C-CA
• rs56354395
• NM_004797.4:c.*372dupA

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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:40648): (ADIPOQ antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.*372dupA		3_prime_UTR_variant	Exon 3 of 3	ENST00000320741.7	NP_004788.1
ADIPOQ-AS1	NR_046662.2	n.1177dupT		non_coding_transcript_exon_variant	Exon 2 of 4
ADIPOQ	NM_001177800.2	c.*372dupA		3_prime_UTR_variant	Exon 4 of 4		NP_001171271.1

Ensembl

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

African (AFR) AF: 0.407 AC: 2055 AN: 5054

American (AMR) AF: 0.484 AC: 3629 AN: 7498

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 2114 AN: 4446

East Asian (EAS) AF: 0.402 AC: 2909 AN: 7230

South Asian (SAS) AF: 0.630 AC: 20384 AN: 32340

European-Finnish (FIN) AF: 0.624 AC: 4941 AN: 7922

Middle Eastern (MID) AF: 0.457 AC: 298 AN: 652

European-Non Finnish (NFE) AF: 0.600 AC: 62504 AN: 104154

Other (OTH) AF: 0.571 AC: 5047 AN: 8844

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

African (AFR) AF: 0.435 AC: 17993 AN: 41408

American (AMR) AF: 0.490 AC: 7486 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1734 AN: 3466

East Asian (EAS) AF: 0.424 AC: 2185 AN: 5150

South Asian (SAS) AF: 0.646 AC: 3117 AN: 4822

European-Finnish (FIN) AF: 0.645 AC: 6813 AN: 10562

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42122 AN: 67938

Other (OTH) AF: 0.512 AC: 1082 AN: 2114

Alfa AF: 0.593 Hom.: 3279

Bravo AF: 0.532

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.035
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs56354395; hg19: chr3-186572864;