19-51225385-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001772.4(CD33):āc.205A>Gā(p.Arg69Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 1,613,862 control chromosomes in the GnomAD database, including 134,591 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001772.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD33 | NM_001772.4 | c.205A>G | p.Arg69Gly | missense_variant | 2/7 | ENST00000262262.5 | NP_001763.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD33 | ENST00000262262.5 | c.205A>G | p.Arg69Gly | missense_variant | 2/7 | 1 | NM_001772.4 | ENSP00000262262.3 |
Frequencies
GnomAD3 genomes AF: 0.415 AC: 62996AN: 151928Hom.: 13695 Cov.: 31
GnomAD3 exomes AF: 0.349 AC: 87652AN: 251434Hom.: 17236 AF XY: 0.351 AC XY: 47678AN XY: 135892
GnomAD4 exome AF: 0.398 AC: 581802AN: 1461816Hom.: 120883 Cov.: 46 AF XY: 0.395 AC XY: 287313AN XY: 727212
GnomAD4 genome AF: 0.415 AC: 63034AN: 152046Hom.: 13708 Cov.: 31 AF XY: 0.405 AC XY: 30132AN XY: 74326
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 22, 2019 | This variant is associated with the following publications: (PMID: 30917570) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at