chr18-22171736-C-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_005257.6(GATA6):āc.592C>Gā(p.Leu198Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000096 in 1,469,042 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L198M) has been classified as Uncertain significance.
Frequency
Consequence
NM_005257.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA6 | NM_005257.6 | c.592C>G | p.Leu198Val | missense_variant | 2/7 | ENST00000269216.10 | |
GATA6 | XM_047437483.1 | c.592C>G | p.Leu198Val | missense_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA6 | ENST00000269216.10 | c.592C>G | p.Leu198Val | missense_variant | 2/7 | 1 | NM_005257.6 | P1 | |
GATA6 | ENST00000581694.1 | c.592C>G | p.Leu198Val | missense_variant | 1/6 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000587 AC: 89AN: 151700Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000662 AC: 5AN: 75480Hom.: 0 AF XY: 0.0000682 AC XY: 3AN XY: 43994
GnomAD4 exome AF: 0.0000395 AC: 52AN: 1317234Hom.: 0 Cov.: 30 AF XY: 0.0000338 AC XY: 22AN XY: 650502
GnomAD4 genome AF: 0.000586 AC: 89AN: 151808Hom.: 0 Cov.: 32 AF XY: 0.000647 AC XY: 48AN XY: 74194
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 09, 2020 | This variant is associated with the following publications: (PMID: 20581743) - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2023 | GATA6: PP3, BS1 - |
Tetralogy of Fallot Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 2010 | - - |
Monogenic diabetes Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Personalized Diabetes Medicine Program, University of Maryland School of Medicine | May 18, 2018 | ACMG criteria: PP3 (6 predictors, REVEL = 0.716), [BP4 (3 predictors)], BS3 (PMID 20581743), previously reported in a child with tetralogy of Fallot and this child has pulmonary stenosis = VUS - |
Atrioventricular septal defect 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at