chr10-8054743-T-TAA
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001002295.2(GATA3):c.-503_-502dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.34 ( 7553 hom., cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
GATA3
NM_001002295.2 5_prime_UTR
NM_001002295.2 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.75
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 -8 ACMG points.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GATA3 | NM_001002295.2 | c.-503_-502dup | 5_prime_UTR_variant | 1/6 | ENST00000379328.9 | NP_001002295.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GATA3 | ENST00000379328.9 | c.-503_-502dup | 5_prime_UTR_variant | 1/6 | 1 | NM_001002295.2 | ENSP00000368632 | A1 | ||
GATA3 | ENST00000481743.2 | c.-369-529_-369-528dup | intron_variant | 2 | ENSP00000493486 | |||||
GATA3 | ENST00000643001.1 | c.-369-529_-369-528dup | intron_variant | ENSP00000494284 |
Frequencies
GnomAD3 genomes AF: 0.340 AC: 44862AN: 131820Hom.: 7548 Cov.: 0
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 2Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 2
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GnomAD4 genome AF: 0.340 AC: 44861AN: 131808Hom.: 7553 Cov.: 0 AF XY: 0.339 AC XY: 21271AN XY: 62820
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Hypoparathyroidism, deafness, renal disease syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at