10-8069446-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001002295.2(GATA3):c.925-27C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 1,606,638 control chromosomes in the GnomAD database, including 483,999 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_001002295.2 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GATA3 | ENST00000379328.9 | c.925-27C>T | intron_variant | Intron 4 of 5 | 1 | NM_001002295.2 | ENSP00000368632.3 | |||
GATA3 | ENST00000346208.4 | c.922-27C>T | intron_variant | Intron 4 of 5 | 1 | ENSP00000341619.3 | ||||
GATA3 | ENST00000461472.1 | c.443-27C>T | intron_variant | Intron 1 of 2 | 3 | ENSP00000515407.1 |
Frequencies
GnomAD3 genomes AF: 0.774 AC: 116869AN: 150936Hom.: 45328 Cov.: 26
GnomAD3 exomes AF: 0.806 AC: 202332AN: 251036Hom.: 82029 AF XY: 0.806 AC XY: 109416AN XY: 135686
GnomAD4 exome AF: 0.774 AC: 1127126AN: 1455586Hom.: 438645 Cov.: 34 AF XY: 0.777 AC XY: 562880AN XY: 724524
GnomAD4 genome AF: 0.774 AC: 116943AN: 151052Hom.: 45354 Cov.: 26 AF XY: 0.778 AC XY: 57400AN XY: 73732
ClinVar
Submissions by phenotype
not provided Benign:2
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Hypoparathyroidism, deafness, renal disease syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at