chr18-22171192-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_005257.6(GATA6):c.48C>A(p.Ala16=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000688 in 1,599,714 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A16A) has been classified as Likely benign.
Frequency
Consequence
NM_005257.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA6 | NM_005257.6 | c.48C>A | p.Ala16= | synonymous_variant | 2/7 | ENST00000269216.10 | |
GATA6 | XM_047437483.1 | c.48C>A | p.Ala16= | synonymous_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA6 | ENST00000269216.10 | c.48C>A | p.Ala16= | synonymous_variant | 2/7 | 1 | NM_005257.6 | P1 | |
GATA6 | ENST00000581694.1 | c.48C>A | p.Ala16= | synonymous_variant | 1/6 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151948Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000131 AC: 3AN: 229602Hom.: 0 AF XY: 0.00000785 AC XY: 1AN XY: 127386
GnomAD4 exome AF: 0.00000691 AC: 10AN: 1447766Hom.: 0 Cov.: 31 AF XY: 0.00000555 AC XY: 4AN XY: 720826
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151948Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74186
ClinVar
Submissions by phenotype
Atrioventricular septal defect 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at