19-51225502-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001772.4(CD33):c.322G>A(p.Ala108Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000639 in 1,612,916 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001772.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152186Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000116 AC: 29AN: 249470Hom.: 0 AF XY: 0.000170 AC XY: 23AN XY: 134986
GnomAD4 exome AF: 0.0000657 AC: 96AN: 1460612Hom.: 1 Cov.: 33 AF XY: 0.0000922 AC XY: 67AN XY: 726572
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152304Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.322G>A (p.A108T) alteration is located in exon 2 (coding exon 2) of the CD33 gene. This alteration results from a G to A substitution at nucleotide position 322, causing the alanine (A) at amino acid position 108 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at