rs9957475
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005257.6(GATA6):c.1303-503T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 151,004 control chromosomes in the GnomAD database, including 5,052 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.15 ( 5052 hom., cov: 32)
Consequence
GATA6
NM_005257.6 intron
NM_005257.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.46
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA6 | NM_005257.6 | c.1303-503T>C | intron_variant | ENST00000269216.10 | |||
GATA6 | XM_047437483.1 | c.1303-503T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA6 | ENST00000269216.10 | c.1303-503T>C | intron_variant | 1 | NM_005257.6 | P1 | |||
GATA6 | ENST00000581694.1 | c.1303-503T>C | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.154 AC: 23300AN: 150884Hom.: 5033 Cov.: 32
GnomAD3 genomes
?
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23300
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150884
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.155 AC: 23374AN: 151004Hom.: 5052 Cov.: 32 AF XY: 0.152 AC XY: 11182AN XY: 73722
GnomAD4 genome
?
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23374
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151004
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32
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11182
AN XY:
73722
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Asia WGS
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342
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at