rs6141488

Positions:

• chr20-34604942-C-G

Variant summary

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

The NM_080476.5(PIGU):​c.627+11100G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,790 control chromosomes in the GnomAD database, including 10,359 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 0.36 (10359 hom., cov: 30)
• Consequence: PIGU NM_080476.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIGU	NM_080476.5	c.627+11100G>C		intron_variant		ENST00000217446.8
PIGU	XM_017027664.2	c.627+11100G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIGU	ENST00000217446.8	c.627+11100G>C		intron_variant		1	NM_080476.5	P1
PIGU	ENST00000374820.6	c.567+11100G>C		intron_variant		1
PIGU	ENST00000438215.1	c.52+11100G>C		intron_variant		3
PIGU	ENST00000480175.1	n.90-16335G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55056 AN: 151672 Hom.: 10336 Cov.: 30

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.363 AC: 55128 AN: 151790 Hom.: 10359 Cov.: 30 AF XY: 0.364 AC XY: 26963 AN XY: 74140

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.392

Alfa AF: 0.342 Hom.: 1147

Bravo AF: 0.386

Asia WGS AF: 0.343 AC: 1190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6141488; hg19: chr20-33192746;