chr20-33629720-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001032999.3(CBFA2T2):c.1034C>T(p.Ala345Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,611,322 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001032999.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CBFA2T2 | NM_001032999.3 | c.1034C>T | p.Ala345Val | missense_variant, splice_region_variant | Exon 8 of 11 | ENST00000342704.11 | NP_001028171.1 | |
CBFA2T2 | NM_005093.4 | c.1061C>T | p.Ala354Val | missense_variant, splice_region_variant | Exon 9 of 12 | NP_005084.1 | ||
CBFA2T2 | NM_001039709.2 | c.974C>T | p.Ala325Val | missense_variant, splice_region_variant | Exon 8 of 11 | NP_001034798.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000105 AC: 26AN: 248668Hom.: 0 AF XY: 0.0000892 AC XY: 12AN XY: 134454
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1459060Hom.: 1 Cov.: 30 AF XY: 0.0000276 AC XY: 20AN XY: 725924
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152262Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1061C>T (p.A354V) alteration is located in exon 9 (coding exon 8) of the CBFA2T2 gene. This alteration results from a C to T substitution at nucleotide position 1061, causing the alanine (A) at amino acid position 354 to be replaced by a valine (V). 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