rs3764962
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005257.6(GATA6):c.1620+7A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0481 in 1,597,168 control chromosomes in the GnomAD database, including 16,033 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005257.6 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATA6 | NM_005257.6 | c.1620+7A>G | splice_region_variant, intron_variant | ENST00000269216.10 | |||
GATA6 | XM_047437483.1 | c.1620+7A>G | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATA6 | ENST00000269216.10 | c.1620+7A>G | splice_region_variant, intron_variant | 1 | NM_005257.6 | P1 | |||
GATA6 | ENST00000581694.1 | c.1620+7A>G | splice_region_variant, intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.192 AC: 29177AN: 152026Hom.: 8319 Cov.: 32
GnomAD3 exomes AF: 0.0690 AC: 17332AN: 251094Hom.: 3529 AF XY: 0.0556 AC XY: 7553AN XY: 135744
GnomAD4 exome AF: 0.0329 AC: 47574AN: 1445024Hom.: 7672 Cov.: 29 AF XY: 0.0307 AC XY: 22088AN XY: 720064
GnomAD4 genome AF: 0.192 AC: 29277AN: 152144Hom.: 8361 Cov.: 32 AF XY: 0.187 AC XY: 13939AN XY: 74388
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 10, 2023 | - - |
Atrioventricular septal defect 5 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at