3-186856375-T-C

Position:

• chr3-186856375-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_004797.4(ADIPOQ):​c.*1671T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.85 in 152,152 control chromosomes in the GnomAD database, including 55,172 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 0.85 (55172 hom., cov: 34)
  • Failed GnomAD Quality Control
• Consequence: ADIPOQ NM_004797.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.*1671T>C		3_prime_UTR_variant	3/3	ENST00000320741.7	NP_004788.1
ADIPOQ-AS1	NR_046662.2	n.137-259A>G		intron_variant, non_coding_transcript_variant
ADIPOQ	NM_001177800.2	c.*1671T>C		3_prime_UTR_variant	4/4		NP_001171271.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.*1671T>C		3_prime_UTR_variant	3/3	1	NM_004797.4	ENSP00000320709	P1
ADIPOQ	ENST00000444204.2	c.*1671T>C		3_prime_UTR_variant	4/4	1		ENSP00000389814	P1

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129214 AN: 152032 Hom.: 55160 Cov.: 34

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.850 AC: 129269 AN: 152152 Hom.: 55172 Cov.: 34 AF XY: 0.849 AC XY: 63154 AN XY: 74406

Gnomad4 AFR AF: 0.794

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.867

Gnomad4 FIN AF: 0.957

Gnomad4 NFE AF: 0.891

Gnomad4 OTH AF: 0.810

Alfa AF: 0.878 Hom.: 6875

Bravo AF: 0.836

Asia WGS AF: 0.777 AC: 2703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	9.3
DANN	Benign	0.91

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: rs2082940; hg19: chr3-186574164;