rs1058240
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001002295.2(GATA3):c.*612G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 233,718 control chromosomes in the GnomAD database, including 79,772 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.81 ( 50536 hom., cov: 34)
Exomes 𝑓: 0.84 ( 29236 hom. )
Consequence
GATA3
NM_001002295.2 3_prime_UTR
NM_001002295.2 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.463
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
?
Variant 10-8074635-G-A is Benign according to our data. Variant chr10-8074635-G-A is described in ClinVar as [Benign]. Clinvar id is 301140.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA3 | NM_001002295.2 | c.*612G>A | 3_prime_UTR_variant | 6/6 | ENST00000379328.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA3 | ENST00000379328.9 | c.*612G>A | 3_prime_UTR_variant | 6/6 | 1 | NM_001002295.2 | A1 | ||
GATA3 | ENST00000346208.4 | c.*612G>A | 3_prime_UTR_variant | 6/6 | 1 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.814 AC: 123734AN: 152098Hom.: 50495 Cov.: 34
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GnomAD4 exome AF: 0.844 AC: 68779AN: 81502Hom.: 29236 Cov.: 0 AF XY: 0.844 AC XY: 31688AN XY: 37526
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GnomAD4 genome ? AF: 0.814 AC: 123832AN: 152216Hom.: 50536 Cov.: 34 AF XY: 0.818 AC XY: 60855AN XY: 74434
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hypoparathyroidism, deafness, renal disease syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at