rs634801

chr9-35098011-C-Achr9-35098011-C-G

Variant summary

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

The ENST00000431804.1(PIGO-AS1):n.295C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,954 control chromosomes in the GnomAD database, including 16,577 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 0.45 (16576 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: PIGO-AS1 ENST00000431804.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148

Genes affected

PIGO-AS1 (HGNC:55692): (PIGO antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIGO-AS1	ENST00000431804.1	n.295C>A		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68578 AN: 151826 Hom.: 16577 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.469

GnomAD4 exome AF: 0.500 AC: 5 AN: 10 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 3 AN XY: 6

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.451 AC: 68592 AN: 151944 Hom.: 16576 Cov.: 32 AF XY: 0.448 AC XY: 33263 AN XY: 74232

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.464

Alfa AF: 0.515 Hom.: 11677

Bravo AF: 0.449

Asia WGS AF: 0.265 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.7
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: rs634801; hg19: chr9-35098008;