chr20-38218246-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001029864.2(KIAA1755):c.2677G>A(p.Ala893Thr) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000889 in 1,461,824 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001029864.2 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIAA1755 | NM_001029864.2 | c.2677G>A | p.Ala893Thr | missense_variant, splice_region_variant | 12/14 | ENST00000279024.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA1755 | ENST00000279024.9 | c.2677G>A | p.Ala893Thr | missense_variant, splice_region_variant | 12/14 | 5 | NM_001029864.2 | P2 | |
KIAA1755 | ENST00000435901.1 | c.574G>A | p.Ala192Thr | missense_variant, splice_region_variant | 5/6 | 5 | |||
KIAA1755 | ENST00000484362.1 | n.956G>A | splice_region_variant, non_coding_transcript_exon_variant | 3/5 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251426Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135886
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461824Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727222
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.2677G>A (p.A893T) alteration is located in exon 12 (coding exon 12) of the KIAA1755 gene. This alteration results from a G to A substitution at nucleotide position 2677, causing the alanine (A) at amino acid position 893 to be replaced by a threonine (T). 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