17-16233930-TA-T

Variant summary

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

The NM_004278.4(PIGL):c.236-29del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 832,566 control chromosomes in the GnomAD database, including 556 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.052 (222 hom., cov: 30)
  • Exomes 𝑓: 0.18 (334 hom.)
• Consequence: PIGL NM_004278.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0720

Genes affected

PIGL (HGNC:8966): (phosphatidylinositol glycan anchor biosynthesis class L) This gene encodes an enzyme that catalyzes the second step of glycosylphosphatidylinositol (GPI) biosynthesis, which is the de-N-acetylation of N-acetylglucosaminylphosphatidylinositol (GlcNAc-PI). Study of a similar rat enzyme suggests that this protein localizes to the endoplasmic reticulum. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-16233930-TA-T is Benign according to our data. Variant chr17-16233930-TA-T is described in ClinVar as [Benign]. Clinvar id is 1294986.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIGL	NM_004278.4	c.236-29del		intron_variant		ENST00000225609.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIGL	ENST00000225609.10	c.236-29del		intron_variant		1	NM_004278.4	P1

Frequencies

GnomAD3 genomes AF: 0.0521 AC: 7582 AN: 145478 Hom.: 223 Cov.: 30

Gnomad AFR AF: 0.0960

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0494

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.0715

Gnomad SAS AF: 0.0463

Gnomad FIN AF: 0.0498

Gnomad MID AF: 0.0229

Gnomad NFE AF: 0.0273

Gnomad OTH AF: 0.0564

GnomAD4 exome AF: 0.182 AC: 125000 AN: 687016 Hom.: 334 Cov.: 0 AF XY: 0.187 AC XY: 65291 AN XY: 348706

Gnomad4 AFR exome AF: 0.238

Gnomad4 AMR exome AF: 0.252

Gnomad4 ASJ exome AF: 0.238

Gnomad4 EAS exome AF: 0.264

Gnomad4 SAS exome AF: 0.251

Gnomad4 FIN exome AF: 0.215

Gnomad4 NFE exome AF: 0.163

Gnomad4 OTH exome AF: 0.203

GnomAD4 genome AF: 0.0521 AC: 7583 AN: 145550 Hom.: 222 Cov.: 30 AF XY: 0.0525 AC XY: 3712 AN XY: 70758

Gnomad4 AFR AF: 0.0957

Gnomad4 AMR AF: 0.0494

Gnomad4 ASJ AF: 0.0277

Gnomad4 EAS AF: 0.0715

Gnomad4 SAS AF: 0.0467

Gnomad4 FIN AF: 0.0498

Gnomad4 NFE AF: 0.0273

Gnomad4 OTH AF: 0.0559

Bravo AF: 0.0534

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

May 24, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs371823707; hg19: chr17-16137244;