rs752993685
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001143979.2(NDE1):c.-340T>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 213,612 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001143979.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NDE1 | NM_001143979.2 | c.-340T>A | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 10 | NP_001137451.1 | |||
NDE1 | XM_006720897.5 | c.-122T>A | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 8 | XP_006720960.1 | |||
NDE1 | XM_047434258.1 | c.-122T>A | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 8 | XP_047290214.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NDE1 | ENST00000396355 | c.-340T>A | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 10 | 1 | ENSP00000379643.1 | ||||
NDE1 | ENST00000396355 | c.-340T>A | 5_prime_UTR_variant | Exon 1 of 10 | 1 | ENSP00000379643.1 | ||||
NDE1 | ENST00000674888.1 | n.-218T>A | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 10 | ENSP00000501936.1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152136Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.000130 AC: 8AN: 61476Hom.: 0 Cov.: 0 AF XY: 0.000149 AC XY: 5AN XY: 33470
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74334
ClinVar
Submissions by phenotype
Lissencephaly 4 Uncertain:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at