rs369673069
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_032638.5(GATA2):c.729C>T(p.His243=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,613,980 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 Likely benign (★★).
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000011 ( 0 hom. )
Consequence
GATA2
NM_032638.5 synonymous
NM_032638.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.45
Genes affected
GATA2 (HGNC:4171): (GATA binding protein 2) This gene encodes a member of the GATA family of zinc-finger transcription factors that are named for the consensus nucleotide sequence they bind in the promoter regions of target genes. The encoded protein plays an essential role in regulating transcription of genes involved in the development and proliferation of hematopoietic and endocrine cell lineages. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
?
Variant 3-128485869-G-A is Benign according to our data. Variant chr3-128485869-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 539724.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=1.45 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000138 (21/152194) while in subpopulation AFR AF= 0.000459 (19/41438). AF 95% confidence interval is 0.0003. There are 0 homozygotes in gnomad4. There are 8 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 21 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA2 | NM_001145661.2 | c.729C>T | p.His243= | synonymous_variant | 4/7 | ENST00000487848.6 | |
GATA2 | NM_032638.5 | c.729C>T | p.His243= | synonymous_variant | 3/6 | ENST00000341105.7 | |
GATA2 | NM_001145662.1 | c.729C>T | p.His243= | synonymous_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA2 | ENST00000341105.7 | c.729C>T | p.His243= | synonymous_variant | 3/6 | 1 | NM_032638.5 | P1 | |
GATA2 | ENST00000487848.6 | c.729C>T | p.His243= | synonymous_variant | 4/7 | 1 | NM_001145661.2 | P1 | |
GATA2 | ENST00000430265.6 | c.729C>T | p.His243= | synonymous_variant | 3/6 | 1 | |||
GATA2 | ENST00000696466.1 | c.1011C>T | p.His337= | synonymous_variant | 5/8 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152194Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250654Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135660
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GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461786Hom.: 0 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 727182
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GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74340
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
GATA2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 17, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Deafness-lymphedema-leukemia syndrome;C3280030:Monocytopenia with susceptibility to infections Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at