4-118054567-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_004784.3(NDST3):c.657C>A(p.Asp219Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,224 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004784.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151914Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461310Hom.: 0 Cov.: 32 AF XY: 0.00000825 AC XY: 6AN XY: 726936
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151914Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74192
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.657C>A (p.D219E) alteration is located in exon 2 (coding exon 1) of the NDST3 gene. This alteration results from a C to A substitution at nucleotide position 657, causing the aspartic acid (D) at amino acid position 219 to be replaced by a glutamic acid (E). 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