rs10489392

Variant names:

• chr1-186485762-A-G
• rs10489392
• ENST00000655945.1:n.784+15367A>G

Variant summary

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

The ENST00000655945.1(PDC-AS1):​n.784+15367A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,176 control chromosomes in the GnomAD database, including 1,033 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 0.11 (1033 hom., cov: 32)
• Consequence: PDC-AS1 ENST00000655945.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

Genes affected

PDC-AS1 (HGNC:40432): (PDC antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDC-AS1	ENST00000655945.1	n.784+15367A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16891 AN: 152058 Hom.: 1025 Cov.: 32

Gnomad AFR AF: 0.0921

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0405

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0674

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.111 AC: 16907 AN: 152176 Hom.: 1033 Cov.: 32 AF XY: 0.108 AC XY: 8040 AN XY: 74418

Gnomad4 AFR AF: 0.0919

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.0402

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0674

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.138

Alfa AF: 0.121 Hom.: 193

Bravo AF: 0.115

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489392; hg19: chr1-186454894;