9-127787515-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001261.4(CDK9):c.175-3C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000553 in 1,608,438 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001261.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDK9 | NM_001261.4 | c.175-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000373264.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDK9 | ENST00000373264.5 | c.175-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001261.4 | P1 | |||
CDK9 | ENST00000421939.5 | c.526-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 3 | |||||
CDK9 | ENST00000491521.1 | n.16C>T | non_coding_transcript_exon_variant | 1/4 | 3 | ||||
CDK9 | ENST00000480353.5 | n.250-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000954 AC: 24AN: 251442Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135900
GnomAD4 exome AF: 0.0000549 AC: 80AN: 1456144Hom.: 0 Cov.: 29 AF XY: 0.0000497 AC XY: 36AN XY: 724820
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74462
ClinVar
Submissions by phenotype
CDK9-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 28, 2023 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at