13-52012444-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_StrongBS1
The NM_001004127.3(ALG11):c.26G>T(p.Cys9Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000128 in 1,614,100 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C9S) has been classified as Likely benign.
Frequency
Consequence
NM_001004127.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000996 AC: 25AN: 251050Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135824
GnomAD4 exome AF: 0.000130 AC: 190AN: 1461752Hom.: 0 Cov.: 30 AF XY: 0.000118 AC XY: 86AN XY: 727148
GnomAD4 genome AF: 0.000112 AC: 17AN: 152348Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74488
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at