8-11748803-T-C
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001308093.3(GATA4):c.617-113T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 1,276,656 control chromosomes in the GnomAD database, including 374,717 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001308093.3 intron
Scores
Clinical Significance
Conservation
Publications
- atrial septal defect 2Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
- structural congenital heart disease, multiple types - GATA4Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- testicular anomalies with or without congenital heart diseaseInheritance: AD Classification: DEFINITIVE Submitted by: Ambry Genetics
- metabolic syndromeInheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
- neonatal diabetes mellitusInheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
- pancreatic hypoplasia-diabetes-congenital heart disease syndromeInheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
- permanent neonatal diabetes mellitusInheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
- transient neonatal diabetes mellitusInheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
- 46,XY partial gonadal dysgenesisInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- familial atrial fibrillationInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- tetralogy of fallotInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- dilated cardiomyopathyInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.804 AC: 122250AN: 152134Hom.: 49742 Cov.: 33 show subpopulations
GnomAD4 exome AF: 0.756 AC: 849976AN: 1124404Hom.: 324915 AF XY: 0.759 AC XY: 436396AN XY: 575192 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.804 AC: 122370AN: 152252Hom.: 49802 Cov.: 33 AF XY: 0.813 AC XY: 60534AN XY: 74452 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Benign:4
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While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.833, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error. -
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not provided Benign:3
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Congenital heart disease Pathogenic:1Benign:1
NG_008177.2(NM_002052.4):c.617-116T>C in the gene GATA4 has an allele frequency of 0.898 in African subpopulation in the gnomAD database. 128 homozygous occurrences are observed in the gnomAD database. This evidence suggests the variant to be classified as benign. ACMG/AMP criteria applied: BA1, BS2. -
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Structural congenital heart disease, multiple types - GATA4 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at