16-58503844-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001242835.2(NDRG4):c.68G>A(p.Arg23Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000787 in 1,613,756 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R23W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001242835.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDRG4 | NM_001242835.2 | c.68G>A | p.Arg23Gln | missense_variant | 2/15 | ENST00000570248.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NDRG4 | ENST00000570248.6 | c.68G>A | p.Arg23Gln | missense_variant | 2/15 | 1 | NM_001242835.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152040Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251208Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135812
GnomAD4 exome AF: 0.0000835 AC: 122AN: 1461716Hom.: 0 Cov.: 32 AF XY: 0.0000729 AC XY: 53AN XY: 727146
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152040Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 17, 2024 | The c.224G>A (p.R75Q) alteration is located in exon 4 (coding exon 4) of the NDRG4 gene. This alteration results from a G to A substitution at nucleotide position 224, causing the arginine (R) at amino acid position 75 to be replaced by a glutamine (Q). 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