rs771739064
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_032638.5(GATA2):āc.1185T>Cā(p.Thr395=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,613,974 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 ā ). Synonymous variant affecting the same amino acid position (i.e. T395T) 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 -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA2 | NM_001145661.2 | c.1185T>C | p.Thr395= | synonymous_variant | 7/7 | ENST00000487848.6 | |
GATA2 | NM_032638.5 | c.1185T>C | p.Thr395= | synonymous_variant | 6/6 | ENST00000341105.7 | |
GATA2 | NM_001145662.1 | c.1143T>C | p.Thr381= | synonymous_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA2 | ENST00000341105.7 | c.1185T>C | p.Thr395= | synonymous_variant | 6/6 | 1 | NM_032638.5 | P1 | |
GATA2 | ENST00000487848.6 | c.1185T>C | p.Thr395= | synonymous_variant | 7/7 | 1 | NM_001145661.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000956 AC: 24AN: 251174Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135766
GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461810Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727208
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74338
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 21, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2022 | GATA2: BP4, BP7 - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Apr 08, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at