rs10489392

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0919 AC: 3816 AN: 41514

American (AMR) AF: 0.122 AC: 1856 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 740 AN: 3468

East Asian (EAS) AF: 0.0402 AC: 208 AN: 5174

South Asian (SAS) AF: 0.117 AC: 566 AN: 4824

European-Finnish (FIN) AF: 0.0674 AC: 715 AN: 10608

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8638 AN: 67996

Other (OTH) AF: 0.138 AC: 292 AN: 2116

Alfa AF: 0.122 Hom.: 203

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10489392; hg19: chr1-186454894;