19-18257823-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001145304.2(IQCN):c.3461G>A(p.Arg1154Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,611,004 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 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. R1154G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001145304.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IQCN | NM_001145304.2 | c.3461G>A | p.Arg1154Gln | missense_variant | 4/4 | ENST00000392413.5 | |
IQCN | NM_025249.4 | c.2900G>A | p.Arg967Gln | missense_variant | 4/4 | ||
IQCN | NM_001145305.2 | c.2762G>A | p.Arg921Gln | missense_variant | 4/4 | ||
IQCN | XM_005260084.2 | c.3461G>A | p.Arg1154Gln | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQCN | ENST00000392413.5 | c.3461G>A | p.Arg1154Gln | missense_variant | 4/4 | 1 | NM_001145304.2 | A2 | |
IQCN | ENST00000600328.7 | c.2900G>A | p.Arg967Gln | missense_variant | 4/4 | 1 | P2 | ||
IQCN | ENST00000600359.7 | c.2762G>A | p.Arg921Gln | missense_variant | 4/4 | 2 | A2 | ||
IQCN | ENST00000599638.2 | n.4796G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000818 AC: 2AN: 244390Hom.: 0 AF XY: 0.00000749 AC XY: 1AN XY: 133466
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1458804Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 725698
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152200Hom.: 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 | Feb 16, 2023 | The c.3461G>A (p.R1154Q) alteration is located in exon 4 (coding exon 3) of the KIAA1683 gene. This alteration results from a G to A substitution at nucleotide position 3461, causing the arginine (R) at amino acid position 1154 to be replaced by a glutamine (Q). 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