chr16-85077446-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001388359.1(KIAA0513):c.596C>T(p.Pro199Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000589 in 1,614,074 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001388359.1 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 |
---|---|---|---|---|---|---|---|
KIAA0513 | NM_001388359.1 | c.596C>T | p.Pro199Leu | missense_variant | 6/13 | ENST00000683363.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA0513 | ENST00000683363.1 | c.596C>T | p.Pro199Leu | missense_variant | 6/13 | NM_001388359.1 | A1 | ||
KIAA0513 | ENST00000566428.5 | c.596C>T | p.Pro199Leu | missense_variant | 6/13 | 1 | A1 | ||
KIAA0513 | ENST00000567328.6 | c.596C>T | p.Pro199Leu | missense_variant | 6/8 | 1 | |||
KIAA0513 | ENST00000538274.6 | c.596C>T | p.Pro199Leu | missense_variant | 6/12 | 2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000439 AC: 11AN: 250710Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135732
GnomAD4 exome AF: 0.0000609 AC: 89AN: 1461776Hom.: 0 Cov.: 32 AF XY: 0.0000536 AC XY: 39AN XY: 727204
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152298Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2021 | The c.596C>T (p.P199L) alteration is located in exon 6 (coding exon 5) of the KIAA0513 gene. This alteration results from a C to T substitution at nucleotide position 596, causing the proline (P) at amino acid position 199 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at