5-157460218-CTCGC-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001099287.2(NIPAL4):c.-103_-99delCTCGCinsT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001099287.2 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Variant summary: NIPAL4 c.84_88delinsT (p.Ser29AlafsX133) results in a frameshift in the first exon of the longest protein isoform (NM_001099287.1) of NIPAL4. However, the variant is located in the untranslated mRNA region (c.-103_-99delinsT) upstream of the initiation codon in the shorter (canonical) protein isoform (NM_001099287.2) of NIPAL4. The variant was absent in 125568 control chromosomes (gnomAD). To our knowledge, no occurrence of c.84_88delinsT in individuals affected with Lamellar Ichthyosis and no experimental evidence demonstrating its impact on protein function have been reported. However, upstream from this position, a start-loss variant affecting the longer isoform, c.2T>C (p.Met1?), has been reported in a homozygous patient (PMID: 31347739; this variant would correspond to c.-185T>C in the shorter isoform). No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.