rs764984

chr17-16313674-G-Cchr17-16313674-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_004278.4(PIGL):c.494+60G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0328 in 1,302,380 control chromosomes in the GnomAD database, including 901 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.047 (205 hom., cov: 33)
  • Exomes 𝑓: 0.031 (696 hom.)
• Consequence: PIGL NM_004278.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.245

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 17-16313674-G-C is Benign according to our data. Variant chr17-16313674-G-C is described in ClinVar as [Benign]. Clinvar id is 1262840.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PIGL	NM_004278.4	c.494+60G>C		intron_variant		ENST00000225609.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PIGL	ENST00000225609.10	c.494+60G>C		intron_variant		1	NM_004278.4	P1

Frequencies

GnomAD3 genomes AF: 0.0469 AC: 7134 AN: 152046 Hom.: 206 Cov.: 33

Gnomad AFR AF: 0.0850

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0446

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.0623

Gnomad SAS AF: 0.0431

Gnomad FIN AF: 0.0395

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0261

Gnomad OTH AF: 0.0517

GnomAD4 exome AF: 0.0309 AC: 35583 AN: 1150216 Hom.: 696 AF XY: 0.0310 AC XY: 18099 AN XY: 584750

Gnomad4 AFR exome AF: 0.0867

Gnomad4 AMR exome AF: 0.0482

Gnomad4 ASJ exome AF: 0.0284

Gnomad4 EAS exome AF: 0.0446

Gnomad4 SAS exome AF: 0.0430

Gnomad4 FIN exome AF: 0.0389

Gnomad4 NFE exome AF: 0.0254

Gnomad4 OTH exome AF: 0.0381

GnomAD4 genome AF: 0.0469 AC: 7137 AN: 152164 Hom.: 205 Cov.: 33 AF XY: 0.0465 AC XY: 3461 AN XY: 74396

Gnomad4 AFR AF: 0.0848

Gnomad4 AMR AF: 0.0446

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.0623

Gnomad4 SAS AF: 0.0433

Gnomad4 FIN AF: 0.0395

Gnomad4 NFE AF: 0.0262

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.00820 Hom.: 3

Bravo AF: 0.0494

Asia WGS AF: 0.0490 AC: 173 AN: 3478

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

Jun 17, 2019

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	8.0
Dann	Benign	0.54

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: rs764984; hg19: chr17-16216988;