11-10752665-A-AT
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PVS1_ModerateBP6_ModerateBS1BS2
The NM_014633.5(CTR9):c.46-3dupT variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000305 in 1,604,746 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_014633.5 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CTR9 | ENST00000361367.7 | c.46-7_46-6insT | splice_region_variant, intron_variant | Intron 1 of 24 | 1 | NM_014633.5 | ENSP00000355013.2 | |||
CTR9 | ENST00000524523.1 | c.7-7_7-6insT | splice_region_variant, intron_variant | Intron 1 of 7 | 5 | ENSP00000431458.1 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 250140Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135160
GnomAD4 exome AF: 0.0000165 AC: 24AN: 1452538Hom.: 0 Cov.: 27 AF XY: 0.0000180 AC XY: 13AN XY: 723146
GnomAD4 genome AF: 0.000164 AC: 25AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74374
ClinVar
Submissions by phenotype
CTR9-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at