rs760132552
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_032638.5(GATA2):āc.16G>Cā(p.Glu6Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000245 in 1,594,650 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E6K) has been classified as Uncertain significance.
Frequency
Consequence
NM_032638.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA2 | NM_001145661.2 | c.16G>C | p.Glu6Gln | missense_variant | 3/7 | ENST00000487848.6 | |
GATA2 | NM_032638.5 | c.16G>C | p.Glu6Gln | missense_variant | 2/6 | ENST00000341105.7 | |
GATA2 | NM_001145662.1 | c.16G>C | p.Glu6Gln | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA2 | ENST00000341105.7 | c.16G>C | p.Glu6Gln | missense_variant | 2/6 | 1 | NM_032638.5 | P1 | |
GATA2 | ENST00000487848.6 | c.16G>C | p.Glu6Gln | missense_variant | 3/7 | 1 | NM_001145661.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000766 AC: 16AN: 208742Hom.: 0 AF XY: 0.0000617 AC XY: 7AN XY: 113408
GnomAD4 exome AF: 0.0000250 AC: 36AN: 1442454Hom.: 0 Cov.: 32 AF XY: 0.0000224 AC XY: 16AN XY: 715660
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
Acute myeloid leukemia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Dec 31, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at