chr17-16233930-TA-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
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
NM_004278.4 intron
Scores
Not classified
Clinical Significance
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]
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ACMG classification
Classification made for transcript
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: 7582AN: 145478Hom.: 223 Cov.: 30
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GnomAD4 exome AF: 0.182 AC: 125000AN: 687016Hom.: 334 Cov.: 0 AF XY: 0.187 AC XY: 65291AN XY: 348706
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GnomAD4 genome AF: 0.0521 AC: 7583AN: 145550Hom.: 222 Cov.: 30 AF XY: 0.0525 AC XY: 3712AN XY: 70758
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 24, 2021 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at