16-15643558-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_001143979.2(NDE1):c.-535C>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 0.000495 in 337,086 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001143979.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NDE1 | NM_001143979.2 | c.-535C>A | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 10 | NP_001137451.1 | |||
NDE1 | XM_006720897.5 | c.-317C>A | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 8 | XP_006720960.1 | |||
NDE1 | XM_047434258.1 | c.-317C>A | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 8 | XP_047290214.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000751 AC: 114AN: 151746Hom.: 1 Cov.: 31
GnomAD4 exome AF: 0.000286 AC: 53AN: 185230Hom.: 0 Cov.: 0 AF XY: 0.000317 AC XY: 34AN XY: 107272
GnomAD4 genome AF: 0.000751 AC: 114AN: 151856Hom.: 1 Cov.: 31 AF XY: 0.000714 AC XY: 53AN XY: 74204
ClinVar
Submissions by phenotype
Lissencephaly 4 Benign: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 and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at