18-62087057-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_176787.5(PIGN):​c.2370+1699G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 151,756 control chromosomes in the GnomAD database, including 4,683 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 0.24 ( 4683 hom., cov: 31)

Consequence

PIGN
NM_176787.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.75
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PIGNNM_176787.5 linkc.2370+1699G>A intron_variant ENST00000640252.2 NP_789744.1 O95427A0A024R2C3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PIGNENST00000640252.2 linkc.2370+1699G>A intron_variant 1 NM_176787.5 ENSP00000492233.1 O95427
PIGNENST00000400334.7 linkc.2370+1699G>A intron_variant 1 ENSP00000383188.2 O95427
PIGNENST00000638424.1 linkn.*338+1334G>A intron_variant 5 ENSP00000491963.1 A0A1W2PQZ1

Frequencies

GnomAD3 genomes
AF:
0.245
AC:
37106
AN:
151638
Hom.:
4676
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.237
Gnomad AMI
AF:
0.294
Gnomad AMR
AF:
0.213
Gnomad ASJ
AF:
0.227
Gnomad EAS
AF:
0.0911
Gnomad SAS
AF:
0.167
Gnomad FIN
AF:
0.259
Gnomad MID
AF:
0.234
Gnomad NFE
AF:
0.272
Gnomad OTH
AF:
0.248
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.245
AC:
37124
AN:
151756
Hom.:
4683
Cov.:
31
AF XY:
0.242
AC XY:
17977
AN XY:
74154
show subpopulations
Gnomad4 AFR
AF:
0.237
Gnomad4 AMR
AF:
0.213
Gnomad4 ASJ
AF:
0.227
Gnomad4 EAS
AF:
0.0915
Gnomad4 SAS
AF:
0.166
Gnomad4 FIN
AF:
0.259
Gnomad4 NFE
AF:
0.272
Gnomad4 OTH
AF:
0.248
Alfa
AF:
0.236
Hom.:
2027
Bravo
AF:
0.240
Asia WGS
AF:
0.150
AC:
523
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.14
DANN
Benign
0.77

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs663354; hg19: chr18-59754290; API