17-81902378-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_148896.5(NPB):c.101C>T(p.Ser34Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000447 in 1,343,014 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_148896.5 missense
Scores
Clinical Significance
Conservation
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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 |
---|---|---|---|---|---|---|---|---|---|---|
NPB | ENST00000333383.8 | c.101C>T | p.Ser34Phe | missense_variant | Exon 1 of 2 | 1 | NM_148896.5 | ENSP00000332766.7 | ||
PCYT2 | ENST00000538936 | c.*2455G>A | 3_prime_UTR_variant | Exon 13 of 13 | 1 | NM_002861.5 | ENSP00000439245.3 | |||
NPB | ENST00000573081.1 | c.101C>T | p.Ser34Phe | missense_variant | Exon 1 of 1 | 6 | ENSP00000461824.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152078Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000336 AC: 4AN: 1190936Hom.: 0 Cov.: 31 AF XY: 0.00000349 AC XY: 2AN XY: 573210
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152078Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.101C>T (p.S34F) alteration is located in exon 1 (coding exon 1) of the NPB gene. This alteration results from a C to T substitution at nucleotide position 101, causing the serine (S) at amino acid position 34 to be replaced by a phenylalanine (F). 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