rs1321306

Variant names:

• chr20-34678575-T-A
• rs1321306
• ENST00000628281.2:n.96+20120A>T

Your query was ambiguous. Multiple possible variants found:

• 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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PIGU	ENST00000628281.2	n.96+20120A>T		intron_variant	Intron 1 of 6	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;