chr17-47531409-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_006310.4(NPEPPS):c.109C>T(p.Leu37Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000769 in 1,547,232 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NPEPPS | NM_006310.4 | c.109C>T | p.Leu37Phe | missense_variant | 1/23 | ENST00000322157.9 | |
NPEPPS | NM_001411130.1 | c.109C>T | p.Leu37Phe | missense_variant | 1/24 | ||
NPEPPS | NM_001330257.2 | c.97C>T | p.Leu33Phe | missense_variant | 2/24 | ||
NPEPPS | XM_017025373.1 | c.97C>T | p.Leu33Phe | missense_variant | 2/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NPEPPS | ENST00000322157.9 | c.109C>T | p.Leu37Phe | missense_variant | 1/23 | 1 | NM_006310.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000726 AC: 11AN: 151426Hom.: 0 Cov.: 26
GnomAD3 exomes AF: 0.000109 AC: 16AN: 146546Hom.: 0 AF XY: 0.0000761 AC XY: 6AN XY: 78840
GnomAD4 exome AF: 0.0000774 AC: 108AN: 1395700Hom.: 0 Cov.: 32 AF XY: 0.0000697 AC XY: 48AN XY: 688432
GnomAD4 genome ? AF: 0.0000726 AC: 11AN: 151532Hom.: 0 Cov.: 26 AF XY: 0.0000810 AC XY: 6AN XY: 74034
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2022 | The c.109C>T (p.L37F) alteration is located in exon 1 (coding exon 1) of the NPEPPS gene. This alteration results from a C to T substitution at nucleotide position 109, causing the leucine (L) at amino acid position 37 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