3-186860685-C-T

Variant names:

• chr3-186860685-C-T
• rs7639352
• NR_046662.2:n.136+548G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_046662.2(ADIPOQ-AS1):​n.136+548G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,966 control chromosomes in the GnomAD database, including 6,207 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 0.29 (6207 hom., cov: 33)
• Consequence: ADIPOQ-AS1 NR_046662.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.781
• Publications: 16 publications found

Genes affected

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADIPOQ-AS1	NR_046662.2	n.136+548G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43553 AN: 151848 Hom.: 6204 Cov.: 33

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.287 AC: 43567 AN: 151966 Hom.: 6207 Cov.: 33 AF XY: 0.287 AC XY: 21289 AN XY: 74272

African (AFR) AF: 0.304 AC: 12578 AN: 41414

American (AMR) AF: 0.301 AC: 4600 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1067 AN: 3470

East Asian (EAS) AF: 0.297 AC: 1538 AN: 5176

South Asian (SAS) AF: 0.248 AC: 1194 AN: 4824

European-Finnish (FIN) AF: 0.313 AC: 3290 AN: 10512

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18388 AN: 67994

Other (OTH) AF: 0.286 AC: 604 AN: 2112

Alfa AF: 0.244 Hom.: 1472

Bravo AF: 0.284

Asia WGS AF: 0.286 AC: 992 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.64
PhyloP100		-0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7639352; hg19: chr3-186578474;