rs377027316
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002778.4(PSAP):c.409C>T(p.Leu137Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,614,034 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L137V) has been classified as Likely benign.
Frequency
Consequence
NM_002778.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSAP | NM_002778.4 | c.409C>T | p.Leu137Phe | missense_variant | 5/14 | ENST00000394936.8 | |
PSAP | NM_001042465.3 | c.409C>T | p.Leu137Phe | missense_variant | 5/15 | ||
PSAP | NM_001042466.3 | c.409C>T | p.Leu137Phe | missense_variant | 5/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSAP | ENST00000394936.8 | c.409C>T | p.Leu137Phe | missense_variant | 5/14 | 1 | NM_002778.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251334Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135874
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461866Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727236
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at