9-137040820-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015392.4(NPDC1):c.550G>A(p.Ala184Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000339 in 1,592,864 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
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NPDC1 | ENST00000371601.5 | c.550G>A | p.Ala184Thr | missense_variant | Exon 4 of 9 | 1 | NM_015392.4 | ENSP00000360660.4 | ||
NPDC1 | ENST00000371600.7 | c.784G>A | p.Ala262Thr | missense_variant | Exon 3 of 8 | 1 | ENSP00000360659.3 | |||
NPDC1 | ENST00000488145.1 | n.694G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000285 AC: 6AN: 210842Hom.: 0 AF XY: 0.0000431 AC XY: 5AN XY: 116092
GnomAD4 exome AF: 0.0000354 AC: 51AN: 1440664Hom.: 0 Cov.: 34 AF XY: 0.0000363 AC XY: 26AN XY: 715786
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.550G>A (p.A184T) 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 550, causing the alanine (A) at amino acid position 184 to be replaced by a threonine (T). 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