chr20-38217393-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001029864.2(KIAA1755):c.2761C>T(p.Arg921Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,613,256 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R921L) 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.2761C>T | p.Arg921Cys | missense_variant | 13/14 | ENST00000279024.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIAA1755 | ENST00000279024.9 | c.2761C>T | p.Arg921Cys | missense_variant | 13/14 | 5 | NM_001029864.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000483 AC: 12AN: 248510Hom.: 0 AF XY: 0.0000446 AC XY: 6AN XY: 134576
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461064Hom.: 0 Cov.: 33 AF XY: 0.0000275 AC XY: 20AN XY: 726740
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2023 | The c.2761C>T (p.R921C) alteration is located in exon 13 (coding exon 13) of the KIAA1755 gene. This alteration results from a C to T substitution at nucleotide position 2761, causing the arginine (R) at amino acid position 921 to be replaced by a cysteine (C). 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