chr10-8073399-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001002295.2(GATA3):c.1051-340C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000829 in 151,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00083 ( 0 hom., cov: 31)
Consequence
GATA3
NM_001002295.2 intron
NM_001002295.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0120
Genes affected
GATA3 (HGNC:4172): (GATA binding protein 3) This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is an important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia. [provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000829 (126/151984) while in subpopulation AFR AF= 0.0028 (116/41436). AF 95% confidence interval is 0.00239. There are 0 homozygotes in gnomad4. There are 64 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High AC in GnomAd4 at 126 AD gene.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GATA3 | ENST00000379328.9 | c.1051-340C>T | intron_variant | 1 | NM_001002295.2 | ENSP00000368632.3 | ||||
GATA3 | ENST00000346208.4 | c.1048-340C>T | intron_variant | 1 | ENSP00000341619.3 | |||||
GATA3 | ENST00000461472.1 | c.569-340C>T | intron_variant | 3 | ENSP00000515407.1 |
Frequencies
GnomAD3 genomes AF: 0.000830 AC: 126AN: 151868Hom.: 0 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.000829 AC: 126AN: 151984Hom.: 0 Cov.: 31 AF XY: 0.000862 AC XY: 64AN XY: 74274
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at