5-94384466-T-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_001145678.3(KIAA0825):c.3620-8A>G variant causes a splice region, intron change. The variant allele was found at a frequency of 0.0178 in 1,547,060 control chromosomes in the GnomAD database, including 331 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001145678.3 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIAA0825 | NM_001145678.3 | c.3620-8A>G | splice_region_variant, intron_variant | Intron 19 of 20 | ENST00000682413.1 | NP_001139150.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIAA0825 | ENST00000682413.1 | c.3620-8A>G | splice_region_variant, intron_variant | Intron 19 of 20 | NM_001145678.3 | ENSP00000506760.1 | ||||
KIAA0825 | ENST00000703867.1 | c.3631-4A>G | splice_region_variant, intron_variant | Intron 19 of 20 | ENSP00000515512.1 | |||||
KIAA0825 | ENST00000513200.7 | c.3616-4A>G | splice_region_variant, intron_variant | Intron 18 of 19 | 5 | ENSP00000424618.2 |
Frequencies
GnomAD3 genomes AF: 0.0143 AC: 2176AN: 152092Hom.: 22 Cov.: 32
GnomAD3 exomes AF: 0.0180 AC: 2833AN: 157424Hom.: 32 AF XY: 0.0194 AC XY: 1609AN XY: 83128
GnomAD4 exome AF: 0.0181 AC: 25288AN: 1394848Hom.: 308 Cov.: 28 AF XY: 0.0187 AC XY: 12883AN XY: 688198
GnomAD4 genome AF: 0.0143 AC: 2177AN: 152212Hom.: 23 Cov.: 32 AF XY: 0.0142 AC XY: 1055AN XY: 74400
ClinVar
Submissions by phenotype
KIAA0825-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at