3-186856493-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• 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 -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004797.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOQ	NM_004797.4	MANE Select	c.*1789C>T		3_prime_UTR	Exon 3 of 3	NP_004788.1
	ADIPOQ	NM_001177800.2		c.*1789C>T		3_prime_UTR	Exon 4 of 4	NP_001171271.1
	ADIPOQ-AS1	NR_046662.2		n.137-377G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADIPOQ	ENST00000320741.7	TSL:1 MANE Select	c.*1789C>T		3_prime_UTR	Exon 3 of 3	ENSP00000320709.2
	ADIPOQ	ENST00000444204.2	TSL:1	c.*1789C>T		3_prime_UTR	Exon 4 of 4	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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0455 AC: 1 AN: 22

Other (OTH) AF: 0.00 AC: 0 AN: 6

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

African (AFR) AF: 0.00993 AC: 412 AN: 41510

American (AMR) AF: 0.0305 AC: 466 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0302 AC: 105 AN: 3472

East Asian (EAS) AF: 0.0281 AC: 146 AN: 5192

South Asian (SAS) AF: 0.0835 AC: 403 AN: 4824

European-Finnish (FIN) AF: 0.0891 AC: 942 AN: 10578

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0592 AC: 4026 AN: 68000

Other (OTH) AF: 0.0417 AC: 88 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.41
PhyloP100		-0.22
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: rs35469083; hg19: chr3-186574282;