rs146624465
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_005257.6(GATA6):c.1320T>A(p.Leu440=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000774 in 1,614,120 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). Synonymous variant affecting the same amino acid position (i.e. L440L) has been classified as Likely benign.
Frequency
Consequence
NM_005257.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA6 | NM_005257.6 | c.1320T>A | p.Leu440= | synonymous_variant | 4/7 | ENST00000269216.10 | |
GATA6 | XM_047437483.1 | c.1320T>A | p.Leu440= | synonymous_variant | 4/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA6 | ENST00000269216.10 | c.1320T>A | p.Leu440= | synonymous_variant | 4/7 | 1 | NM_005257.6 | P1 | |
GATA6 | ENST00000581694.1 | c.1320T>A | p.Leu440= | synonymous_variant | 3/6 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152242Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251492Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135922
GnomAD4 exome AF: 0.0000787 AC: 115AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.0000729 AC XY: 53AN XY: 727238
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74380
ClinVar
Submissions by phenotype
GATA6-related condition Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 01, 2023 | The GATA6 c.1320T>A variant is not predicted to result in an amino acid change (p.=). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0080% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/18-19761431-T-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Atrioventricular septal defect 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 29, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at