20-36665299-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_032013.4(NDRG3):c.695G>A(p.Arg232His) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000103 in 1,614,018 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032013.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NDRG3 | ENST00000349004.6 | c.695G>A | p.Arg232His | missense_variant, splice_region_variant | Exon 11 of 16 | 1 | NM_032013.4 | ENSP00000345292.1 | ||
NDRG3 | ENST00000359675.6 | c.659G>A | p.Arg220His | missense_variant, splice_region_variant | Exon 10 of 15 | 1 | ENSP00000352703.2 | |||
NDRG3 | ENST00000373773.7 | c.410G>A | p.Arg137His | missense_variant, splice_region_variant | Exon 8 of 13 | 1 | ENSP00000362878.3 | |||
NDRG3 | ENST00000373803.6 | c.695G>A | p.Arg232His | missense_variant, splice_region_variant | Exon 11 of 17 | 5 | ENSP00000362909.2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251384Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135870
GnomAD4 exome AF: 0.000106 AC: 155AN: 1461764Hom.: 0 Cov.: 31 AF XY: 0.000105 AC XY: 76AN XY: 727196
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.695G>A (p.R232H) alteration is located in exon 11 (coding exon 10) of the NDRG3 gene. This alteration results from a G to A substitution at nucleotide position 695, causing the arginine (R) at amino acid position 232 to be replaced by a histidine (H). 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