20-38217392-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001029864.2(KIAA1755):c.2762G>T(p.Arg921Leu) 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 1,613,290 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R921C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001029864.2 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 |
---|---|---|---|---|---|---|---|
KIAA1755 | NM_001029864.2 | c.2762G>T | p.Arg921Leu | missense_variant | 13/14 | ENST00000279024.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA1755 | ENST00000279024.9 | c.2762G>T | p.Arg921Leu | missense_variant | 13/14 | 5 | NM_001029864.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248504Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134574
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461080Hom.: 0 Cov.: 33 AF XY: 0.0000179 AC XY: 13AN XY: 726748
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2021 | The c.2762G>T (p.R921L) alteration is located in exon 13 (coding exon 13) of the KIAA1755 gene. This alteration results from a G to T substitution at nucleotide position 2762, causing the arginine (R) at amino acid position 921 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