3-186848537-C-T

Position:

• chr3-186848537-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.-8-4514C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,980 control chromosomes in the GnomAD database, including 7,499 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 0.30 (7499 hom., cov: 31)
• Consequence: ADIPOQ NM_004797.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOQ	NM_004797.4	c.-8-4514C>T		intron_variant		ENST00000320741.7	NP_004788.1
ADIPOQ	NM_001177800.2	c.-9+2930C>T		intron_variant			NP_001171271.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADIPOQ	ENST00000320741.7	c.-8-4514C>T		intron_variant		1	NM_004797.4	ENSP00000320709.2
ADIPOQ	ENST00000444204.2	c.-9+2930C>T		intron_variant		1		ENSP00000389814.2

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46094 AN: 151862 Hom.: 7488 Cov.: 31

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.275

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.304 AC: 46139 AN: 151980 Hom.: 7499 Cov.: 31 AF XY: 0.312 AC XY: 23169 AN XY: 74268

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.276

Alfa AF: 0.282 Hom.: 787

Bravo AF: 0.303

Asia WGS AF: 0.378 AC: 1315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.82

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: rs822393; hg19: chr3-186566326;