9-5919939-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001017969.3(KIAA2026):c.6057G>T(p.Leu2019Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,822 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001017969.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA2026 | NM_001017969.3 | c.6057G>T | p.Leu2019Phe | missense_variant | 8/8 | ENST00000399933.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA2026 | ENST00000399933.8 | c.6057G>T | p.Leu2019Phe | missense_variant | 8/8 | 5 | NM_001017969.3 | P4 | |
KIAA2026 | ENST00000381461.6 | c.5967G>T | p.Leu1989Phe | missense_variant | 7/7 | 5 | A2 | ||
KIAA2026 | ENST00000436015.6 | c.554+605G>T | intron_variant, NMD_transcript_variant | 3 | |||||
KIAA2026 | ENST00000540714.1 | c.*3644G>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249128Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135152
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461690Hom.: 0 Cov.: 35 AF XY: 0.00000275 AC XY: 2AN XY: 727130
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.6057G>T (p.L2019F) alteration is located in exon 8 (coding exon 8) of the KIAA2026 gene. This alteration results from a G to T substitution at nucleotide position 6057, causing the leucine (L) at amino acid position 2019 to be replaced by a phenylalanine (F). 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