19-51225847-CCCGG-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001772.4(CD33):c.466_469delGGCC(p.Gly156ThrfsTer5) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0237 in 1,613,994 control chromosomes in the GnomAD database, including 576 homozygotes. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001772.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0159 AC: 2413AN: 152078Hom.: 25 Cov.: 31
GnomAD3 exomes AF: 0.0142 AC: 3561AN: 251316Hom.: 50 AF XY: 0.0138 AC XY: 1874AN XY: 135814
GnomAD4 exome AF: 0.0245 AC: 35851AN: 1461798Hom.: 551 AF XY: 0.0236 AC XY: 17169AN XY: 727216
GnomAD4 genome AF: 0.0158 AC: 2412AN: 152196Hom.: 25 Cov.: 31 AF XY: 0.0140 AC XY: 1043AN XY: 74424
ClinVar
Submissions by phenotype
CD33-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
CD33: BS1, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at