18-22171177-G-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.33G>A(p.Pro11=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000563 in 1,599,892 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 (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Consequence
GATA6
NM_005257.6 synonymous
NM_005257.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.245
Genes affected
GATA6 (HGNC:4174): (GATA binding protein 6) This gene is a member of a small family of zinc finger transcription factors that play an important role in the regulation of cellular differentiation and organogenesis during vertebrate development. This gene is expressed during early embryogenesis and localizes to endo- and mesodermally derived cells during later embryogenesis and thereby plays an important role in gut, lung, and heart development. Mutations in this gene are associated with several congenital defects. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
?
Variant 18-22171177-G-A is Benign according to our data. Variant chr18-22171177-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1553113.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.245 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA6 | NM_005257.6 | c.33G>A | p.Pro11= | synonymous_variant | 2/7 | ENST00000269216.10 | |
GATA6 | XM_047437483.1 | c.33G>A | p.Pro11= | synonymous_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA6 | ENST00000269216.10 | c.33G>A | p.Pro11= | synonymous_variant | 2/7 | 1 | NM_005257.6 | P1 | |
GATA6 | ENST00000581694.1 | c.33G>A | p.Pro11= | synonymous_variant | 1/6 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152154Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000437 AC: 1AN: 229002Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 127146
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GnomAD4 exome AF: 0.00000414 AC: 6AN: 1447620Hom.: 0 Cov.: 30 AF XY: 0.00000416 AC XY: 3AN XY: 720714
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Atrioventricular septal defect 5 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 25, 2022 | - - |
Computational scores
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Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at