NM_005257.6:c.1374C>T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_005257.6(GATA6):c.1374C>T(p.Asn458Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00393 in 1,614,158 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005257.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GATA6 | ENST00000269216.10 | c.1374C>T | p.Asn458Asn | synonymous_variant | Exon 4 of 7 | 1 | NM_005257.6 | ENSP00000269216.3 | ||
GATA6 | ENST00000581694.1 | c.1374C>T | p.Asn458Asn | synonymous_variant | Exon 3 of 6 | 1 | ENSP00000462313.1 |
Frequencies
GnomAD3 genomes AF: 0.00232 AC: 353AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00217 AC: 546AN: 251484Hom.: 3 AF XY: 0.00246 AC XY: 334AN XY: 135916
GnomAD4 exome AF: 0.00410 AC: 5991AN: 1461860Hom.: 26 Cov.: 32 AF XY: 0.00407 AC XY: 2963AN XY: 727228
GnomAD4 genome AF: 0.00232 AC: 353AN: 152298Hom.: 0 Cov.: 32 AF XY: 0.00226 AC XY: 168AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:4
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GATA6: BP4, BP7, BS1, BS2 -
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not specified Benign:3
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Tetralogy of Fallot;C1857586:Conotruncal heart malformations;C2931296:Pancreatic hypoplasia-diabetes-congenital heart disease syndrome;C3280939:Atrioventricular septal defect 5;C3280943:Atrial septal defect 9 Benign:1
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Atrioventricular septal defect 5 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at