chr1-26787956-G-A
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_017837.4(PIGV):c.-370G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0565 in 152,460 control chromosomes in the GnomAD database, including 320 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.056 ( 319 hom., cov: 32)
Exomes 𝑓: 0.075 ( 1 hom. )
Consequence
PIGV
NM_017837.4 5_prime_UTR
NM_017837.4 5_prime_UTR
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 2.98
Genes affected
PIGV (HGNC:26031): (phosphatidylinositol glycan anchor biosynthesis class V) This gene encodes a mannosyltransferase enzyme involved in the biosynthesis of glycosylphosphatidylinositol (GPI). GPI is a complex glycolipid that functions as a membrane anchor for many proteins and plays a role in multiple cellular processes including protein sorting and signal transduction. The encoded protein is localized to the endoplasmic reticulum and transfers the second mannose to the GPI backbone. Mutations in this gene are associated with hyperphosphatasia cognitive disability syndrome. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant 1-26787956-G-A is Benign according to our data. Variant chr1-26787956-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 368873.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0778 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PIGV | NM_017837.4 | c.-370G>A | 5_prime_UTR_variant | 1/4 | ENST00000674202.1 | NP_060307.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PIGV | ENST00000674202.1 | c.-370G>A | 5_prime_UTR_variant | 1/4 | NM_017837.4 | ENSP00000501479 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0565 AC: 8595AN: 152172Hom.: 318 Cov.: 32
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GnomAD4 exome AF: 0.0747 AC: 13AN: 174Hom.: 1 Cov.: 0 AF XY: 0.0821 AC XY: 11AN XY: 134
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GnomAD4 genome AF: 0.0565 AC: 8601AN: 152286Hom.: 319 Cov.: 32 AF XY: 0.0563 AC XY: 4190AN XY: 74476
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Hyperphosphatasia-intellectual disability syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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Benign
CADD
Benign
DANN
Uncertain
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at