rs376360090
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_032638.5(GATA2):c.1023C>T(p.Ala341=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000057 in 1,613,244 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. A341A) 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.1023C>T | p.Ala341= | synonymous_variant | 6/7 | ENST00000487848.6 | |
GATA2 | NM_032638.5 | c.1023C>T | p.Ala341= | synonymous_variant | 5/6 | ENST00000341105.7 | |
GATA2 | NM_001145662.1 | c.1018-37C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA2 | ENST00000341105.7 | c.1023C>T | p.Ala341= | synonymous_variant | 5/6 | 1 | NM_032638.5 | P1 | |
GATA2 | ENST00000487848.6 | c.1023C>T | p.Ala341= | synonymous_variant | 6/7 | 1 | NM_001145661.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152088Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 249356Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135200
GnomAD4 exome AF: 0.0000609 AC: 89AN: 1461156Hom.: 0 Cov.: 32 AF XY: 0.0000757 AC XY: 55AN XY: 726896
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152088Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74278
ClinVar
Submissions by phenotype
Deafness-lymphedema-leukemia syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Deafness-lymphedema-leukemia syndrome;C3280030:Monocytopenia with susceptibility to infections Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at