1-109164499-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020775.5(ELAPOR1):c.275C>G(p.Ser92Cys) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000243 in 1,606,612 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predict no significant impact on normal splicing. 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. S92Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_020775.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 247340Hom.: 0 AF XY: 0.0000375 AC XY: 5AN XY: 133486
GnomAD4 exome AF: 0.0000206 AC: 30AN: 1454266Hom.: 0 Cov.: 31 AF XY: 0.0000249 AC XY: 18AN XY: 722288
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152346Hom.: 0 Cov.: 32 AF XY: 0.0000805 AC XY: 6AN XY: 74508
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.275C>G (p.S92C) alteration is located in exon 3 (coding exon 3) of the KIAA1324 gene. This alteration results from a C to G substitution at nucleotide position 275, causing the serine (S) at amino acid position 92 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