20-34675229-T-C

Position:

• chr20-34675229-T-C

Variant summary

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

The NM_080476.5(PIGU):​c.130+1727A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.43 (11932 hom., cov: 18)
• Consequence: PIGU NM_080476.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305

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=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIGU	NM_080476.5	c.130+1727A>G		intron_variant		ENST00000217446.8
PIGU	XM_017027664.2	c.130+1727A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIGU	ENST00000217446.8	c.130+1727A>G		intron_variant		1	NM_080476.5	P1
PIGU	ENST00000374820.6	c.130+1727A>G		intron_variant		1
PIGU	ENST00000462389.1	n.135+1727A>G		intron_variant, non_coding_transcript_variant		2
PIGU	ENST00000628281.2	n.97-17985A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.435 AC: 55984 AN: 128788 Hom.: 11917 Cov.: 18

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.435 AC: 56022 AN: 128818 Hom.: 11932 Cov.: 18 AF XY: 0.442 AC XY: 26599 AN XY: 60204

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.468

Alfa AF: 0.215 Hom.: 445

Bravo AF: 0.441

Asia WGS AF: 0.348 AC: 1207 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6087616; hg19: chr20-33263033;