16-15643418-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001143979.2(NDE1):c.-675G>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 0.00655 in 468,038 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001143979.2 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NDE1 | NM_001143979.2 | c.-675G>A | 5_prime_UTR_variant | Exon 1 of 10 | NP_001137451.1 | |||
NDE1 | XM_006720897.5 | c.-457G>A | 5_prime_UTR_variant | Exon 1 of 8 | XP_006720960.1 | |||
NDE1 | XM_047434258.1 | c.-457G>A | 5_prime_UTR_variant | Exon 1 of 8 | XP_047290214.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00533 AC: 811AN: 152190Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00728 AC: 1125AN: 154572Hom.: 12 AF XY: 0.00873 AC XY: 730AN XY: 83596
GnomAD4 exome AF: 0.00709 AC: 2237AN: 315730Hom.: 33 Cov.: 0 AF XY: 0.00886 AC XY: 1600AN XY: 180544
GnomAD4 genome AF: 0.00543 AC: 827AN: 152308Hom.: 12 Cov.: 32 AF XY: 0.00598 AC XY: 445AN XY: 74472
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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at