5-7867917-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024091.4(FASTKD3):c.167A>T(p.Lys56Ile) 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. 15/21 in silico tools predict a benign outcome for this variant. 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. K56R) has been classified as Likely benign.
Frequency
Consequence
NM_024091.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FASTKD3 | NM_024091.4 | c.167A>T | p.Lys56Ile | missense_variant | 2/7 | ENST00000264669.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FASTKD3 | ENST00000264669.10 | c.167A>T | p.Lys56Ile | missense_variant | 2/7 | 2 | NM_024091.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD4 exome Cov.: 67
GnomAD4 genome Cov.: 30
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at