rs913494641
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_032638.5(GATA2):c.684C>T(p.Pro228=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,998 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 (★). Synonymous variant affecting the same amino acid position (i.e. P228P) 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 -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA2 | NM_001145661.2 | c.684C>T | p.Pro228= | synonymous_variant | 4/7 | ENST00000487848.6 | |
GATA2 | NM_032638.5 | c.684C>T | p.Pro228= | synonymous_variant | 3/6 | ENST00000341105.7 | |
GATA2 | NM_001145662.1 | c.684C>T | p.Pro228= | synonymous_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA2 | ENST00000341105.7 | c.684C>T | p.Pro228= | synonymous_variant | 3/6 | 1 | NM_032638.5 | P1 | |
GATA2 | ENST00000487848.6 | c.684C>T | p.Pro228= | synonymous_variant | 4/7 | 1 | NM_001145661.2 | P1 | |
GATA2 | ENST00000430265.6 | c.684C>T | p.Pro228= | synonymous_variant | 3/6 | 1 | |||
GATA2 | ENST00000696466.1 | c.966C>T | p.Pro322= | synonymous_variant | 5/8 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251018Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135788
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461856Hom.: 0 Cov.: 33 AF XY: 0.0000261 AC XY: 19AN XY: 727224
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74314
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 | Nov 05, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at