rs1024528816
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_005257.6(GATA6):c.750C>A(p.Gly250=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000771 in 1,154,314 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. G250G) 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 -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA6 | NM_005257.6 | c.750C>A | p.Gly250= | synonymous_variant | 2/7 | ENST00000269216.10 | |
GATA6 | XM_047437483.1 | c.750C>A | p.Gly250= | synonymous_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA6 | ENST00000269216.10 | c.750C>A | p.Gly250= | synonymous_variant | 2/7 | 1 | NM_005257.6 | P1 | |
GATA6 | ENST00000581694.1 | c.750C>A | p.Gly250= | synonymous_variant | 1/6 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000343 AC: 51AN: 148746Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000378 AC: 38AN: 1005462Hom.: 0 Cov.: 29 AF XY: 0.0000232 AC XY: 11AN XY: 473746
GnomAD4 genome ? AF: 0.000343 AC: 51AN: 148852Hom.: 0 Cov.: 32 AF XY: 0.000331 AC XY: 24AN XY: 72550
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 21, 2020 | - - |
Atrioventricular septal defect 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at