chr19-18257824-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001145304.2(IQCN):āc.3460C>Gā(p.Arg1154Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000807 in 1,610,998 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1154Q) 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.3460C>G | p.Arg1154Gly | missense_variant | 4/4 | ENST00000392413.5 | |
IQCN | NM_025249.4 | c.2899C>G | p.Arg967Gly | missense_variant | 4/4 | ||
IQCN | NM_001145305.2 | c.2761C>G | p.Arg921Gly | missense_variant | 4/4 | ||
IQCN | XM_005260084.2 | c.3460C>G | p.Arg1154Gly | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IQCN | ENST00000392413.5 | c.3460C>G | p.Arg1154Gly | missense_variant | 4/4 | 1 | NM_001145304.2 | A2 | |
IQCN | ENST00000600328.7 | c.2899C>G | p.Arg967Gly | missense_variant | 4/4 | 1 | P2 | ||
IQCN | ENST00000600359.7 | c.2761C>G | p.Arg921Gly | missense_variant | 4/4 | 2 | A2 | ||
IQCN | ENST00000599638.2 | n.4795C>G | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000450 AC: 11AN: 244386Hom.: 0 AF XY: 0.0000375 AC XY: 5AN XY: 133452
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1458812Hom.: 0 Cov.: 31 AF XY: 0.00000551 AC XY: 4AN XY: 725714
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152186Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2023 | The c.3460C>G (p.R1154G) alteration is located in exon 4 (coding exon 3) of the KIAA1683 gene. This alteration results from a C to G substitution at nucleotide position 3460, causing the arginine (R) at amino acid position 1154 to be replaced by a glycine (G). 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