17-49578630-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007225.4(NXPH3):c.89C>T(p.Ser30Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000334 in 1,586,456 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007225.4 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 |
---|---|---|---|---|---|---|---|---|---|---|
NXPH3 | ENST00000328741.6 | c.89C>T | p.Ser30Leu | missense_variant | Exon 2 of 2 | 1 | NM_007225.4 | ENSP00000329295.6 | ||
NXPH3 | ENST00000513748.1 | c.89C>T | p.Ser30Leu | missense_variant | Exon 2 of 3 | 1 | ENSP00000421168.1 | |||
NXPH3 | ENST00000570453.1 | n.-4C>T | upstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000892 AC: 2AN: 224322Hom.: 0 AF XY: 0.00000827 AC XY: 1AN XY: 120910
GnomAD4 exome AF: 0.0000356 AC: 51AN: 1434314Hom.: 0 Cov.: 32 AF XY: 0.0000380 AC XY: 27AN XY: 711358
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.89C>T (p.S30L) alteration is located in exon 2 (coding exon 2) of the NXPH3 gene. This alteration results from a C to T substitution at nucleotide position 89, causing the serine (S) at amino acid position 30 to be replaced by a leucine (L). 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