rs3797799
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005575.3(LNPEP):āc.256T>Cā(p.Ser86Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,614,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005575.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LNPEP | NM_005575.3 | c.256T>C | p.Ser86Pro | missense_variant | 2/18 | ENST00000231368.10 | NP_005566.2 | |
LNPEP | NM_175920.4 | c.214T>C | p.Ser72Pro | missense_variant | 2/18 | NP_787116.2 | ||
LNPEP | XM_047417177.1 | c.256T>C | p.Ser86Pro | missense_variant | 2/16 | XP_047273133.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LNPEP | ENST00000231368.10 | c.256T>C | p.Ser86Pro | missense_variant | 2/18 | 1 | NM_005575.3 | ENSP00000231368.5 | ||
LNPEP | ENST00000395770.3 | c.214T>C | p.Ser72Pro | missense_variant | 2/18 | 1 | ENSP00000379117.3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250690Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135444
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461774Hom.: 0 Cov.: 33 AF XY: 0.0000261 AC XY: 19AN XY: 727188
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74462
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at