chr10-8051222-T-G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000420815.5(GATA3-AS1):n.401+52A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Consequence
GATA3-AS1
ENST00000420815.5 intron
ENST00000420815.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.572
Publications
28 publications found
Genes affected
GATA3-AS1 (HGNC:33786): (GATA3 antisense RNA 1)
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]
GATA3 Gene-Disease associations (from GenCC):
- hypoparathyroidism-deafness-renal disease syndromeInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: PanelApp Australia, G2P, Labcorp Genetics (formerly Invitae), ClinGen, Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GATA3-AS1 | NR_024256.1 | n.1442A>C | non_coding_transcript_exon_variant | Exon 2 of 2 | ||||
GATA3-AS1 | NR_104329.1 | n.502A>C | non_coding_transcript_exon_variant | Exon 2 of 3 | ||||
GATA3 | NM_001441115.1 | c.-369-4065T>G | intron_variant | Intron 1 of 5 | NP_001428044.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GATA3-AS1 | ENST00000420815.5 | n.401+52A>C | intron_variant | Intron 2 of 2 | 1 | |||||
GATA3-AS1 | ENST00000438755.1 | n.426+27A>C | intron_variant | Intron 2 of 2 | 1 | |||||
GATA3-AS1 | ENST00000355358.1 | n.1442A>C | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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