18-62045677-G-GA

Position:

• chr18-62045677-G-GA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_176787.5(PIGN):​c.*178_*179insT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.52 (21959 hom., cov: 0)
  • Exomes 𝑓: 0.52 (36800 hom.)
• Consequence: PIGN NM_176787.5 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.298

Genes affected

PIGN (HGNC:8967): (phosphatidylinositol glycan anchor biosynthesis class N) This gene encodes a protein that is involved in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor is a glycolipid found on many blood cells and serves to anchor proteins to the cell surface. This protein is expressed in the endoplasmic reticulum and transfers phosphoethanolamine (EtNP) to the first mannose of the GPI anchor. Two alternatively spliced variants, which encode an identical isoform, have been reported. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 18-62045677-G-GA is Benign according to our data. Variant chr18-62045677-G-GA is described in ClinVar as [Benign]. Clinvar id is 1224902.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIGN	NM_176787.5	c.*178_*179insT		3_prime_UTR_variant	31/31	ENST00000640252.2	NP_789744.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PIGN	ENST00000640252.2	c.*178_*179insT		3_prime_UTR_variant	31/31	1	NM_176787.5	ENSP00000492233	P1

Frequencies

GnomAD3 genomes AF: 0.515 AC: 77896 AN: 151198 Hom.: 21952 Cov.: 0

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.523

GnomAD4 exome AF: 0.517 AC: 158315 AN: 306490 Hom.: 36800 Cov.: 6 AF XY: 0.517 AC XY: 81643 AN XY: 157882

Gnomad4 AFR exome AF: 0.238

Gnomad4 AMR exome AF: 0.578

Gnomad4 ASJ exome AF: 0.543

Gnomad4 EAS exome AF: 0.592

Gnomad4 SAS exome AF: 0.517

Gnomad4 FIN exome AF: 0.567

Gnomad4 NFE exome AF: 0.514

Gnomad4 OTH exome AF: 0.501

GnomAD4 genome AF: 0.515 AC: 77930 AN: 151314 Hom.: 21959 Cov.: 0 AF XY: 0.523 AC XY: 38665 AN XY: 73894

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.520

Alfa AF: 0.330 Hom.: 705

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 05, 2018

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3833870; hg19: chr18-59712910;