2-3606223-G-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_001255986.1(COLEC11):āc.32G>Cā(p.Cys11Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000356 in 1,550,508 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001255986.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00187 AC: 284AN: 152122Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000497 AC: 73AN: 146758Hom.: 0 AF XY: 0.000392 AC XY: 31AN XY: 79162
GnomAD4 exome AF: 0.000190 AC: 266AN: 1398268Hom.: 0 Cov.: 31 AF XY: 0.000155 AC XY: 107AN XY: 689662
GnomAD4 genome AF: 0.00188 AC: 286AN: 152240Hom.: 1 Cov.: 33 AF XY: 0.00172 AC XY: 128AN XY: 74434
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