chr2-46613765-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_002643.4(PIGF):ā€‹c.249C>Gā€‹(p.Cys83Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000284 in 1,551,808 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.000079 ( 0 hom., cov: 32)
Exomes š‘“: 0.000023 ( 0 hom. )

Consequence

PIGF
NM_002643.4 missense

Scores

1
9
9

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.34
Variant links:
Genes affected
PIGF (HGNC:8962): (phosphatidylinositol glycan anchor biosynthesis class F) This gene encodes a protein involved in glycosylphosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor, a glycolipid containing three mannose molecules in its core backbone, is found on many blood cells where it serves to anchor proteins to the cell surface. The encoded protein and another GPI synthesis protein, PIGO, function in the transfer of ethanolaminephosphate to the third mannose in GPI. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PIGFNM_002643.4 linkuse as main transcriptc.249C>G p.Cys83Trp missense_variant 3/6 ENST00000281382.11 NP_002634.1
PIGFNM_173074.3 linkuse as main transcriptc.249C>G p.Cys83Trp missense_variant 3/7 NP_775097.1
PIGFXM_011532908.4 linkuse as main transcriptc.249C>G p.Cys83Trp missense_variant 3/7 XP_011531210.1
PIGFXM_005264369.4 linkuse as main transcriptc.249C>G p.Cys83Trp missense_variant 3/6 XP_005264426.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PIGFENST00000281382.11 linkuse as main transcriptc.249C>G p.Cys83Trp missense_variant 3/61 NM_002643.4 ENSP00000281382 P1Q07326-1
PIGFENST00000306465.8 linkuse as main transcriptc.249C>G p.Cys83Trp missense_variant 3/71 ENSP00000302663 Q07326-2
PIGFENST00000495933.1 linkuse as main transcriptn.3266C>G non_coding_transcript_exon_variant 1/22
PIGFENST00000412717.1 linkuse as main transcriptc.228+1172C>G intron_variant, NMD_transcript_variant 3 ENSP00000413202

Frequencies

GnomAD3 genomes
AF:
0.0000854
AC:
13
AN:
152164
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000193
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000769
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000822
AC:
19
AN:
231270
Hom.:
0
AF XY:
0.0000641
AC XY:
8
AN XY:
124776
show subpopulations
Gnomad AFR exome
AF:
0.000277
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000747
Gnomad SAS exome
AF:
0.0000363
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.000175
GnomAD4 exome
AF:
0.0000229
AC:
32
AN:
1399526
Hom.:
0
Cov.:
23
AF XY:
0.0000143
AC XY:
10
AN XY:
698198
show subpopulations
Gnomad4 AFR exome
AF:
0.000156
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000434
Gnomad4 SAS exome
AF:
0.0000121
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.000155
GnomAD4 genome
AF:
0.0000788
AC:
12
AN:
152282
Hom.:
0
Cov.:
32
AF XY:
0.0000806
AC XY:
6
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.000192
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000578
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000712
Hom.:
0
Bravo
AF:
0.000121
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000495
AC:
6
Asia WGS
AF:
0.000866
AC:
3
AN:
3478

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsFeb 28, 2023The c.249C>G (p.C83W) alteration is located in exon 3 (coding exon 2) of the PIGF gene. This alteration results from a C to G substitution at nucleotide position 249, causing the cysteine (C) at amino acid position 83 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.41
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Uncertain
-0.050
CADD
Uncertain
25
DANN
Uncertain
0.99
DEOGEN2
Benign
0.11
T;.
Eigen
Uncertain
0.42
Eigen_PC
Uncertain
0.41
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Benign
0.85
D;T
M_CAP
Benign
0.0045
T
MetaRNN
Uncertain
0.52
D;D
MetaSVM
Benign
-0.65
T
MutationAssessor
Uncertain
2.4
M;M
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.54
T
PROVEAN
Benign
-1.9
N;N
REVEL
Uncertain
0.46
Sift
Benign
0.10
T;D
Sift4G
Benign
0.18
T;T
Polyphen
0.99
D;D
Vest4
0.79
MVP
0.74
MPC
0.018
ClinPred
0.16
T
GERP RS
3.3
Varity_R
0.80
gMVP
0.79

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: rs370717506; hg19: chr2-46840904; API