rs570531959
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_032638.5(GATA2):c.208G>T(p.Val70Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000218 in 1,608,808 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. V70V) has been classified as Likely benign.
Frequency
Consequence
NM_032638.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA2 | NM_001145661.2 | c.208G>T | p.Val70Phe | missense_variant | 3/7 | ENST00000487848.6 | |
GATA2 | NM_032638.5 | c.208G>T | p.Val70Phe | missense_variant | 2/6 | ENST00000341105.7 | |
GATA2 | NM_001145662.1 | c.208G>T | p.Val70Phe | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA2 | ENST00000341105.7 | c.208G>T | p.Val70Phe | missense_variant | 2/6 | 1 | NM_032638.5 | P1 | |
GATA2 | ENST00000487848.6 | c.208G>T | p.Val70Phe | missense_variant | 3/7 | 1 | NM_001145661.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152280Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000892 AC: 21AN: 235372Hom.: 0 AF XY: 0.0000705 AC XY: 9AN XY: 127720
GnomAD4 exome AF: 0.0000220 AC: 32AN: 1456410Hom.: 0 Cov.: 32 AF XY: 0.0000207 AC XY: 15AN XY: 724002
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152398Hom.: 0 Cov.: 33 AF XY: 0.0000268 AC XY: 2AN XY: 74522
ClinVar
Submissions by phenotype
Acute myeloid leukemia;C3279664:Deafness-lymphedema-leukemia syndrome;C3280030:Monocytopenia with susceptibility to infections;C3463824:Myelodysplastic syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago | Oct 28, 2022 | This variant has not been reported in the literature but is present in the Genome Aggregation Database (Highest reported MAF 0.1% (20/17588) (https://gnomad.broadinstitute.org/variant/3-128205667-C-A?dataset=gnomad_r2_1). This variant is present in ClinVar (Variation ID:472452). Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. - |
Acute myeloid leukemia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Jul 31, 2023 | - - |
Deafness-lymphedema-leukemia syndrome;C3280030:Monocytopenia with susceptibility to infections Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 20, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at