19-47479873-C-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_007059.4(KPTN):c.777G>T(p.Ser259=) variant causes a synonymous 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. S259S) has been classified as Likely benign.
Frequency
Consequence
NM_007059.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KPTN | NM_007059.4 | c.777G>T | p.Ser259= | synonymous_variant | 8/12 | ENST00000338134.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KPTN | ENST00000338134.8 | c.777G>T | p.Ser259= | synonymous_variant | 8/12 | 1 | NM_007059.4 | P1 | |
KPTN | ENST00000595554.1 | c.609G>T | p.Ser203= | synonymous_variant | 6/8 | 3 | |||
KPTN | ENST00000600271.5 | c.57G>T | p.Ser19= | synonymous_variant | 9/10 | 5 | |||
KPTN | ENST00000594208.5 | c.*411G>T | 3_prime_UTR_variant, NMD_transcript_variant | 9/13 | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at