rs371599112
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_032638.5(GATA2):c.1035C>T(p.Ala345=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,613,622 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A345A) 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 -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA2 | NM_001145661.2 | c.1035C>T | p.Ala345= | synonymous_variant | 6/7 | ENST00000487848.6 | |
GATA2 | NM_032638.5 | c.1035C>T | p.Ala345= | synonymous_variant | 5/6 | ENST00000341105.7 | |
GATA2 | NM_001145662.1 | c.1018-25C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA2 | ENST00000341105.7 | c.1035C>T | p.Ala345= | synonymous_variant | 5/6 | 1 | NM_032638.5 | P1 | |
GATA2 | ENST00000487848.6 | c.1035C>T | p.Ala345= | synonymous_variant | 6/7 | 1 | NM_001145661.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250098Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135504
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461452Hom.: 0 Cov.: 32 AF XY: 0.0000206 AC XY: 15AN XY: 727042
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 19, 2016 | - - |
Deafness-lymphedema-leukemia syndrome;C3280030:Monocytopenia with susceptibility to infections Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 25, 2023 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Feb 04, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at