17-8460112-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_030808.5(NDEL1):āc.896A>Gā(p.Asn299Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,614,214 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_030808.5 missense
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NDEL1 | NM_030808.5 | c.896A>G | p.Asn299Ser | missense_variant | 8/9 | ENST00000334527.12 | NP_110435.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NDEL1 | ENST00000334527.12 | c.896A>G | p.Asn299Ser | missense_variant | 8/9 | 1 | NM_030808.5 | ENSP00000333982 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251416Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135878
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461870Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 727236
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152344Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74504
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.896A>G (p.N299S) alteration is located in exon 8 (coding exon 7) of the NDEL1 gene. This alteration results from a A to G substitution at nucleotide position 896, causing the asparagine (N) at amino acid position 299 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at