rs1321306

Positions:

• chr20-34678575-T-A
• chr20-34678575-T-G

Variant summary

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

The ENST00000628281.2(PIGU):​n.96+20120A>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.226

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIGU	ENST00000628281.2	n.96+20120A>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.423

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1321306; hg19: chr20-33266379;