chr3-186856493-C-T

Variant names:

• chr3-186856493-C-T
• rs35469083
• NM_004797.4:c.*1789C>T

Variant summary

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

The NM_004797.4(ADIPOQ):​c.*1789C>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 0.0439 in 152,186 control chromosomes in the GnomAD database, including 224 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 0.044 (224 hom., cov: 32)
  • Exomes 𝑓: 0.033 (0 hom.)
• Consequence: ADIPOQ NM_004797.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.*1789C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000320741.7	NP_004788.1
ADIPOQ	NM_001177800.2	c.*1789C>T		3_prime_UTR_variant	Exon 4 of 4		NP_001171271.1
ADIPOQ-AS1	NR_046662.2	n.137-377G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.*1789C>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_004797.4	ENSP00000320709.2
ADIPOQ	ENST00000444204.2	c.*1789C>T		3_prime_UTR_variant	Exon 4 of 4	1		ENSP00000389814.2

Frequencies

GnomAD3 genomes AF: 0.0439 AC: 6676 AN: 152036 Hom.: 225 Cov.: 32

Gnomad AFR AF: 0.00995

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.0306

Gnomad ASJ AF: 0.0302

Gnomad EAS AF: 0.0281

Gnomad SAS AF: 0.0843

Gnomad FIN AF: 0.0891

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.0412

GnomAD4 exome AF: 0.0333 AC: 1 AN: 30 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 24

Gnomad4 ASJ exome AF: 0.00

Gnomad4 NFE exome AF: 0.0455

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0439 AC: 6673 AN: 152156 Hom.: 224 Cov.: 32 AF XY: 0.0460 AC XY: 3422 AN XY: 74392

Gnomad4 AFR AF: 0.00993

Gnomad4 AMR AF: 0.0305

Gnomad4 ASJ AF: 0.0302

Gnomad4 EAS AF: 0.0281

Gnomad4 SAS AF: 0.0835

Gnomad4 FIN AF: 0.0891

Gnomad4 NFE AF: 0.0592

Gnomad4 OTH AF: 0.0417

Alfa AF: 0.0496 Hom.: 23

Bravo AF: 0.0361

Asia WGS AF: 0.0480 AC: 168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.41

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: rs35469083; hg19: chr3-186574282;