2-3603669-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001255985.1(COLEC11):c.16+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000122 in 1,551,046 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 (no stars).
Frequency
Consequence
NM_001255985.1 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000397 AC: 6AN: 150996Hom.: 0 AF XY: 0.0000494 AC XY: 4AN XY: 80942
GnomAD4 exome AF: 0.000125 AC: 175AN: 1398746Hom.: 0 Cov.: 30 AF XY: 0.000116 AC XY: 80AN XY: 689874
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152300Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74486
ClinVar
Submissions by phenotype
COLEC11-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at