20-34586079-C-T

Position:

• chr20-34586079-C-T

Variant summary

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

The NM_080476.5(PIGU):​c.783-499G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,926 control chromosomes in the GnomAD database, including 15,369 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 0.44 (15369 hom., cov: 32)
• Consequence: PIGU NM_080476.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

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 (NFE) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIGU	NM_080476.5	c.783-499G>A		intron_variant		ENST00000217446.8	NP_536724.1
PIGU	XM_011528542.2	c.135-499G>A		intron_variant			XP_011526844.1
PIGU	XM_017027664.2	c.782+2374G>A		intron_variant			XP_016883153.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIGU	ENST00000217446.8	c.783-499G>A		intron_variant		1	NM_080476.5	ENSP00000217446	P1
PIGU	ENST00000374820.6	c.723-499G>A		intron_variant		1		ENSP00000363953
PIGU	ENST00000438215.1	c.121-599G>A		intron_variant		3		ENSP00000395755
PIGU	ENST00000480175.1	n.244+2374G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67065 AN: 151808 Hom.: 15362 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.442 AC: 67106 AN: 151926 Hom.: 15369 Cov.: 32 AF XY: 0.443 AC XY: 32913 AN XY: 74226

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.453

Alfa AF: 0.459 Hom.: 4481

Bravo AF: 0.422

Asia WGS AF: 0.409 AC: 1423 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	0.23
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2295444; hg19: chr20-33173883;