rs199640729
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_032638.5(GATA2):c.480C>T(p.Thr160=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,611,654 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. T160T) 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.480C>T | p.Thr160= | synonymous_variant | 4/7 | ENST00000487848.6 | |
GATA2 | NM_032638.5 | c.480C>T | p.Thr160= | synonymous_variant | 3/6 | ENST00000341105.7 | |
GATA2 | NM_001145662.1 | c.480C>T | p.Thr160= | synonymous_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA2 | ENST00000341105.7 | c.480C>T | p.Thr160= | synonymous_variant | 3/6 | 1 | NM_032638.5 | P1 | |
GATA2 | ENST00000487848.6 | c.480C>T | p.Thr160= | synonymous_variant | 4/7 | 1 | NM_001145661.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000161 AC: 39AN: 241916Hom.: 0 AF XY: 0.000137 AC XY: 18AN XY: 131294
GnomAD4 exome AF: 0.0000432 AC: 63AN: 1459384Hom.: 0 Cov.: 36 AF XY: 0.0000386 AC XY: 28AN XY: 725776
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74442
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 12, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Deafness-lymphedema-leukemia syndrome;C3280030:Monocytopenia with susceptibility to infections Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 27, 2023 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Apr 14, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at