rs1415762927
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_032638.5(GATA2):āc.1029A>Gā(p.Arg343=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000992 in 1,613,402 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 (ā ). Synonymous variant affecting the same amino acid position (i.e. R343R) has been classified as Likely benign.
Frequency
Consequence
NM_032638.5 synonymous
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.1029A>G | p.Arg343= | synonymous_variant | 6/7 | ENST00000487848.6 | |
GATA2 | NM_032638.5 | c.1029A>G | p.Arg343= | synonymous_variant | 5/6 | ENST00000341105.7 | |
GATA2 | NM_001145662.1 | c.1018-31A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA2 | ENST00000341105.7 | c.1029A>G | p.Arg343= | synonymous_variant | 5/6 | 1 | NM_032638.5 | P1 | |
GATA2 | ENST00000487848.6 | c.1029A>G | p.Arg343= | synonymous_variant | 6/7 | 1 | NM_001145661.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152058Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461344Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 726972
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152058Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74260
ClinVar
Submissions by phenotype
Deafness-lymphedema-leukemia syndrome;C3280030:Monocytopenia with susceptibility to infections Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at