chr17-47531338-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_006310.4(NPEPPS):c.38G>T(p.Arg13Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006310.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPEPPS | NM_006310.4 | c.38G>T | p.Arg13Leu | missense_variant | 1/23 | ENST00000322157.9 | |
NPEPPS | NM_001411130.1 | c.38G>T | p.Arg13Leu | missense_variant | 1/24 | ||
NPEPPS | NM_001330257.2 | c.78-52G>T | intron_variant | ||||
NPEPPS | XM_017025373.1 | c.78-52G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPEPPS | ENST00000322157.9 | c.38G>T | p.Arg13Leu | missense_variant | 1/23 | 1 | NM_006310.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 25
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 7.60e-7 AC: 1AN: 1315288Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 650198
GnomAD4 genome ? Cov.: 25
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2023 | The c.38G>T (p.R13L) alteration is located in exon 1 (coding exon 1) of the NPEPPS gene. This alteration results from a G to T substitution at nucleotide position 38, causing the arginine (R) at amino acid position 13 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
Publications
No publications associated with this variant yet.