rs3735819
Variant summary
Our verdict is Benign. Variant got -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 Benign (★★).
Frequency
Consequence
NM_001308093.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.804 AC: 122250AN: 152134Hom.: 49742 Cov.: 33
GnomAD4 exome AF: 0.756 AC: 849976AN: 1124404Hom.: 324915 AF XY: 0.759 AC XY: 436396AN XY: 575192
GnomAD4 genome AF: 0.804 AC: 122370AN: 152252Hom.: 49802 Cov.: 33 AF XY: 0.813 AC XY: 60534AN XY: 74452
ClinVar
Submissions by phenotype
not specified Benign:3
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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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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at