3-186855400-C-T

Position:

• chr3-186855400-C-T

Variant summary

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

The NM_004797.4(ADIPOQ):​c.*696C>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 0.951 in 153,102 control chromosomes in the GnomAD database, including 69,602 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 0.95 (69015 hom., cov: 28)
  • Exomes 𝑓: 0.99 (587 hom.)
• Consequence: ADIPOQ NM_004797.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.*696C>T		3_prime_UTR_variant	3/3	ENST00000320741.7	NP_004788.1
ADIPOQ-AS1	NR_046662.2	n.853G>A		non_coding_transcript_exon_variant	2/4
ADIPOQ	NM_001177800.2	c.*696C>T		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.*696C>T		3_prime_UTR_variant	3/3	1	NM_004797.4	ENSP00000320709	P1
ADIPOQ	ENST00000444204.2	c.*696C>T		3_prime_UTR_variant	4/4	1		ENSP00000389814	P1
ADIPOQ-AS1	ENST00000422718.1	n.724G>A		non_coding_transcript_exon_variant	1/3	5

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144362 AN: 151798 Hom.: 68998 Cov.: 28

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.973

Gnomad ASJ AF: 0.998

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.987

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.967

GnomAD4 exome AF: 0.995 AC: 1180 AN: 1186 Hom.: 587 Cov.: 0 AF XY: 0.993 AC XY: 703 AN XY: 708

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.972

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.958

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.999

Gnomad4 OTH exome AF: 0.964

GnomAD4 genome AF: 0.951 AC: 144422 AN: 151916 Hom.: 69015 Cov.: 28 AF XY: 0.952 AC XY: 70620 AN XY: 74178

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.973

Gnomad4 ASJ AF: 0.998

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.988

Gnomad4 FIN AF: 0.999

Gnomad4 NFE AF: 0.996

Gnomad4 OTH AF: 0.967

Alfa AF: 0.983 Hom.: 61181

Bravo AF: 0.944

Asia WGS AF: 0.980 AC: 3406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.47

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: rs6444174; hg19: chr3-186573189;