8-11703355-C-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001308094.2(GATA4):c.-6+2577C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000131 in 152,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00013 ( 0 hom., cov: 33)
Consequence
GATA4
NM_001308094.2 intron
NM_001308094.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.454
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=-0.55).
BP6
Variant 8-11703355-C-A is Benign according to our data. Variant chr8-11703355-C-A is described in ClinVar as [Benign]. Clinvar id is 539983.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.000131 (20/152130) while in subpopulation EAS AF= 0.00174 (9/5164). AF 95% confidence interval is 0.000909. There are 0 homozygotes in gnomad4. There are 12 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 20 AD gene.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| GATA4 | ENST00000532977.1 | c.-458+2577C>A | intron_variant | Intron 2 of 2 | 1 | ENSP00000473671.1 | ||||
| GATA4 | ENST00000528712.5 | c.-6+2577C>A | intron_variant | Intron 2 of 6 | 2 | ENSP00000435043.1 | ||||
| GATA4 | ENST00000526974.1 | c.-458+2577C>A | intron_variant | Intron 2 of 2 | 2 | ENSP00000473598.1 |
Frequencies
GnomAD3 genomes 0.000131 AC: 20AN: 152130Hom.: 0 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.000131 AC: 20AN: 152130Hom.: 0 Cov.: 33 AF XY: 0.000162 AC XY: 12AN XY: 74296
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Atrioventricular septal defect 4 Benign:1
Jul 25, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at