19-51225365-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_001772.4(CD33):c.185G>A(p.Arg62Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000276 in 1,614,186 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001772.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00137 AC: 209AN: 152194Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000374 AC: 94AN: 251460Hom.: 0 AF XY: 0.000272 AC XY: 37AN XY: 135900
GnomAD4 exome AF: 0.000157 AC: 229AN: 1461874Hom.: 1 Cov.: 34 AF XY: 0.000146 AC XY: 106AN XY: 727238
GnomAD4 genome AF: 0.00142 AC: 217AN: 152312Hom.: 1 Cov.: 32 AF XY: 0.00160 AC XY: 119AN XY: 74480
ClinVar
Submissions by phenotype
not provided Benign:2
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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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at