chr3-186859338-G-A

Position:

• chr3-186859338-G-A

Variant summary

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

The NR_046662.2(ADIPOQ-AS1):​n.136+1895C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0178 in 152,094 control chromosomes in the GnomAD database, including 166 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 0.018 (166 hom., cov: 32)
• Consequence: ADIPOQ-AS1 NR_046662.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770

Genes affected

ADIPOQ-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADIPOQ-AS1	NR_046662.2	n.136+1895C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0179 AC: 2713 AN: 151978 Hom.: 167 Cov.: 32

Gnomad AFR AF: 0.00230

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0794

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.00237

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00319

Gnomad OTH AF: 0.0191

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

GnomAD4 genome AF: 0.0178 AC: 2713 AN: 152094 Hom.: 166 Cov.: 32 AF XY: 0.0209 AC XY: 1550 AN XY: 74340

Gnomad4 AFR AF: 0.00229

Gnomad4 AMR AF: 0.0797

Gnomad4 ASJ AF: 0.0115

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.0102

Gnomad4 FIN AF: 0.00237

Gnomad4 NFE AF: 0.00319

Gnomad4 OTH AF: 0.0189

Alfa AF: 0.0172 Hom.: 13

Bravo AF: 0.0244

Asia WGS AF: 0.0800 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12629945; hg19: chr3-186577127;