9-137040843-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015392.4(NPDC1):c.527G>A(p.Arg176Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000376 in 1,596,672 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 (★).
Frequency
Consequence
NM_015392.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPDC1 | ENST00000371601.5 | c.527G>A | p.Arg176Gln | missense_variant | Exon 4 of 9 | 1 | NM_015392.4 | ENSP00000360660.4 | ||
NPDC1 | ENST00000371600.7 | c.761G>A | p.Arg254Gln | missense_variant | Exon 3 of 8 | 1 | ENSP00000360659.3 | |||
NPDC1 | ENST00000488145.1 | n.671G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000230 AC: 5AN: 217764Hom.: 0 AF XY: 0.0000251 AC XY: 3AN XY: 119760
GnomAD4 exome AF: 0.0000339 AC: 49AN: 1444364Hom.: 0 Cov.: 34 AF XY: 0.0000293 AC XY: 21AN XY: 717866
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.527G>A (p.R176Q) alteration is located in exon 4 (coding exon 4) of the NPDC1 gene. This alteration results from a G to A substitution at nucleotide position 527, causing the arginine (R) at amino acid position 176 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