rs3781093
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001002295.2(GATA3):c.778+1123T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,096 control chromosomes in the GnomAD database, including 3,087 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001002295.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Our verdict: Benign. The variant received -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GATA3 | ENST00000379328.9 | c.778+1123T>C | intron_variant | Intron 3 of 5 | 1 | NM_001002295.2 | ENSP00000368632.3 | |||
GATA3 | ENST00000346208.4 | c.778+1123T>C | intron_variant | Intron 3 of 5 | 1 | ENSP00000341619.3 | ||||
GATA3 | ENST00000461472.1 | c.442+1123T>C | intron_variant | Intron 1 of 2 | 3 | ENSP00000515407.1 |
Frequencies
GnomAD3 genomes AF: 0.193 AC: 29376AN: 151978Hom.: 3080 Cov.: 33 show subpopulations
GnomAD4 genome AF: 0.193 AC: 29396AN: 152096Hom.: 3087 Cov.: 33 AF XY: 0.199 AC XY: 14792AN XY: 74348 show subpopulations
ClinVar
Submissions by phenotype
B-cell childhood acute lymphoblastic leukemia Benign:1
No clasiffication has been reported for this variant. However in the Mexican population, we have identified that the C allele was more frequent in children with acute lymphoblastic leukemia (ALL) than controls. In different populations this variant is associated with susceptibility to developing childhood ALL. We clearly observed that the C allele was associated with the risk of developing ALL in Mexican children. These results would be the first to demostrate the association between this variant and the disease in our country. Based on ACMG Guidelines 2015, this varians could be classified as BS1 (Allele frequency is greater than expected for disorder). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at