chr8-11755236-G-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001308093.3(GATA4):c.1000+103G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00066 in 914,874 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00028 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00074 ( 7 hom. )
Consequence
GATA4
NM_001308093.3 intron
NM_001308093.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0990
Genes affected
GATA4 (HGNC:4173): (GATA binding protein 4) This gene encodes a member of the GATA family of zinc-finger transcription factors. Members of this family recognize the GATA motif which is present in the promoters of many genes. This protein is thought to regulate genes involved in embryogenesis and in myocardial differentiation and function, and is necessary for normal testicular development. Mutations in this gene have been associated with cardiac septal defects. Additionally, alterations in gene expression have been associated with several cancer types. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
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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=-0.83).
BP6
Variant 8-11755236-G-T is Benign according to our data. Variant chr8-11755236-G-T is described in ClinVar as [Benign]. Clinvar id is 433019.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000282 (43/152302) while in subpopulation SAS AF= 0.00311 (15/4830). AF 95% confidence interval is 0.00191. There are 0 homozygotes in gnomad4. There are 27 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 43 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA4 | NM_001308093.3 | c.1000+103G>T | intron_variant | ENST00000532059.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA4 | ENST00000532059.6 | c.1000+103G>T | intron_variant | 1 | NM_001308093.3 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000283 AC: 43AN: 152184Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.000736 AC: 561AN: 762572Hom.: 7 AF XY: 0.00100 AC XY: 402AN XY: 400386
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GnomAD4 genome AF: 0.000282 AC: 43AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.000362 AC XY: 27AN XY: 74484
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ClinVar
Significance: Benign
Submissions summary: Pathogenic:1Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Congenital heart disease Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Central Research Laboratory, Sri Devaraj Urs Academy of Higher Education and Research | Jan 07, 2017 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
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