20-34678575-T-A

Variant names:

• chr20-34678575-T-A
• rs1321306
• ENST00000628281.2:n.96+20120A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000628281.2(PIGU):​n.96+20120A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 152,020 control chromosomes in the GnomAD database, including 12,034 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 0.39 (12034 hom., cov: 32)
• Consequence: PIGU ENST00000628281.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226
• Publications: 5 publications found

Genes affected

PIGU (HGNC:15791): (phosphatidylinositol glycan anchor biosynthesis class U) The protein encoded by this gene shares similarity with Saccharomyces cerevisiae Cdc91, a predicted integral membrane protein that may function in cell division control. The protein encoded by this gene is the fifth subunit of GPI transamidase that attaches GPI-anchors to proteins. [provided by RefSeq, Jul 2008]

PIGU Gene-Disease associations (from GenCC):

• glycosylphosphatidylinositol biosynthesis defect 21

  Inheritance: AD, AR Classification: STRONG, MODERATE, LIMITED Submitted by: Illumina, ClinGen, PanelApp Australia, Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000628281.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIGU	ENST00000628281.2	TSL:5	n.96+20120A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59496 AN: 151902 Hom.: 12011 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.392 AC: 59558 AN: 152020 Hom.: 12034 Cov.: 32 AF XY: 0.391 AC XY: 29035 AN XY: 74298

African (AFR) AF: 0.382 AC: 15812 AN: 41442

American (AMR) AF: 0.558 AC: 8505 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1250 AN: 3464

East Asian (EAS) AF: 0.425 AC: 2198 AN: 5174

South Asian (SAS) AF: 0.247 AC: 1194 AN: 4830

European-Finnish (FIN) AF: 0.327 AC: 3453 AN: 10562

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25665 AN: 67990

Other (OTH) AF: 0.423 AC: 895 AN: 2114

Alfa AF: 0.373 Hom.: 1347

Bravo AF: 0.415

Asia WGS AF: 0.340 AC: 1179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.44
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1321306; hg19: chr20-33266379;