rs910873

chr20-34583968-G-Achr20-34583968-G-C

Variant summary

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

The NM_080476.5(PIGU):c.926+1469C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0458 in 152,272 control chromosomes in the GnomAD database, including 262 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 0.046 (262 hom., cov: 31)
• Consequence: PIGU NM_080476.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIGU	NM_080476.5	c.926+1469C>T		intron_variant		ENST00000217446.8
PIGU	XM_011528542.2	c.278+1469C>T		intron_variant
PIGU	XM_017027664.2	c.783-2296C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIGU	ENST00000217446.8	c.926+1469C>T		intron_variant		1	NM_080476.5	P1
PIGU	ENST00000374820.6	c.866+1469C>T		intron_variant		1
PIGU	ENST00000438215.1	c.164+1469C>T		intron_variant		3
PIGU	ENST00000480175.1	n.245-2296C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0458 AC: 6972 AN: 152154 Hom.: 262 Cov.: 31

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0300

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00704

Gnomad FIN AF: 0.0187

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0809

Gnomad OTH AF: 0.0344

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

GnomAD4 genome AF: 0.0458 AC: 6974 AN: 152272 Hom.: 262 Cov.: 31 AF XY: 0.0415 AC XY: 3094 AN XY: 74466

Gnomad4 AFR AF: 0.0145

Gnomad4 AMR AF: 0.0300

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00746

Gnomad4 FIN AF: 0.0187

Gnomad4 NFE AF: 0.0809

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0664 Hom.: 798

Bravo AF: 0.0455

Asia WGS AF: 0.00520 AC: 18 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.71
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs910873; hg19: chr20-33171772;