rs634801

Variant names:

• chr9-35098011-C-A
• rs634801
• ENST00000431804.1:n.295C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-35098011-C-A
• chr9-35098011-C-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000431804.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIGO-AS1	NR_186491.1		n.369C>A		non_coding_transcript_exon	Exon 2 of 2
	PIGO-AS1	NR_186492.1		n.118-1106C>A		intron	N/A
	PIGO-AS1	NR_186493.1		n.117+1591C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIGO-AS1	ENST00000431804.1	TSL:2	n.295C>A		non_coding_transcript_exon	Exon 2 of 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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 4 AN: 8

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.0000000000000565104), which strongly suggests a high chance of mosaicism in these individuals.

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

African (AFR) AF: 0.305 AC: 12613 AN: 41412

American (AMR) AF: 0.532 AC: 8129 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1420 AN: 3470

East Asian (EAS) AF: 0.156 AC: 803 AN: 5162

South Asian (SAS) AF: 0.345 AC: 1661 AN: 4818

European-Finnish (FIN) AF: 0.532 AC: 5601 AN: 10532

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36846 AN: 67950

Other (OTH) AF: 0.464 AC: 980 AN: 2114

Alfa AF: 0.518 Hom.: 15885

Bravo AF: 0.449

Asia WGS AF: 0.265 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.68
PhyloP100		0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs634801;

hg19: chr9-35098008;