GeneBe

rs11471814

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000638967.1(PIGT):​n.1425_1436delACACACACACAC variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000668 in 149,766 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000067 ( 0 hom., cov: 25)

Consequence

PIGT
ENST00000638967.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.984
Variant links:
Genes affected
PIGT (HGNC:14938): (phosphatidylinositol glycan anchor biosynthesis class T) 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 an essential component of the multisubunit enzyme, GPI transamidase. GPI transamidase mediates GPI anchoring in the endoplasmic reticulum, by catalyzing the transfer of fully assembled GPI units to proteins. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, May 2012]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105372631NR_159957.1 linkn.-92_-81delACACACACACAC upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PIGTENST00000638594.1 linkc.1484+2761_1484+2772delACACACACACAC intron_variant Intron 11 of 11 5 ENSP00000491697.1 A0A1W2PPS0
PIGTENST00000638967.1 linkn.1425_1436delACACACACACAC non_coding_transcript_exon_variant Exon 1 of 2 5
PIGTENST00000424705.3 linkn.1485-82_1485-71delACACACACACAC intron_variant Intron 11 of 14 5 ENSP00000491856.2 A0A1W2PPC3

Frequencies

GnomAD3 genomes
AF:
0.00000668
AC:
1
AN:
149766
Hom.:
0
Cov.:
25
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000665
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00000668
AC:
1
AN:
149766
Hom.:
0
Cov.:
25
AF XY:
0.0000137
AC XY:
1
AN XY:
73026
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
40780
American (AMR)
AF:
0.0000665
AC:
1
AN:
15040
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3442
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5034
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4740
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10184
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
312
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67276
Other (OTH)
AF:
0.00
AC:
0
AN:
2058
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
0.00
Hom.:
88

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.98

Splicing

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 for variant 20:45427329 AACACACACACAC>A . It may be empty.

Other links and lift over

dbSNP: rs11471814; hg19: chr20-44055969; API