rs769196688
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_032638.5(GATA2):c.1018-5C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,018 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_032638.5 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA2 | NM_001145661.2 | c.1018-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000487848.6 | |||
GATA2 | NM_032638.5 | c.1018-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000341105.7 | |||
GATA2 | NM_001145662.1 | c.1018-47C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA2 | ENST00000341105.7 | c.1018-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_032638.5 | P1 | |||
GATA2 | ENST00000487848.6 | c.1018-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001145661.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152176Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248826Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 135006
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460842Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726706
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152176Hom.: 1 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74332
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Mar 17, 2023 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this variant does not alter splicing; Has not been previously published as pathogenic or benign to our knowledge - |
Deafness-lymphedema-leukemia syndrome;C3280030:Monocytopenia with susceptibility to infections Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at