5-138345178-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016605.3(FAM53C):c.490C>T(p.Pro164Ser) 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 (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P164A) has been classified as Uncertain significance.
Frequency
Consequence
NM_016605.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAM53C | NM_016605.3 | c.490C>T | p.Pro164Ser | missense_variant | Exon 4 of 5 | ENST00000239906.10 | NP_057689.1 | |
FAM53C | NM_001135647.2 | c.490C>T | p.Pro164Ser | missense_variant | Exon 4 of 5 | NP_001129119.1 | ||
FAM53C | NM_001350195.2 | c.460C>T | p.Pro154Ser | missense_variant | Exon 4 of 5 | NP_001337124.1 | ||
FAM53C | NM_001350194.2 | c.137-280C>T | intron_variant | Intron 3 of 4 | NP_001337123.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at