rs548757932
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_021167.5(GATAD1):c.249+13G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00111 in 1,212,580 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 0.00049 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0012 ( 0 hom. )
Consequence
GATAD1
NM_021167.5 intron
NM_021167.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.824
Genes affected
GATAD1 (HGNC:29941): (GATA zinc finger domain containing 1) The protein encoded by this gene contains a zinc finger at the N-terminus, and is thought to bind to a histone modification site that regulates gene expression. Mutations in this gene have been associated with autosomal recessive dilated cardiomyopathy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 7-92447991-G-A is Benign according to our data. Variant chr7-92447991-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 227372.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GATAD1 | NM_021167.5 | c.249+13G>A | intron_variant | ENST00000287957.5 | NP_066990.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GATAD1 | ENST00000287957.5 | c.249+13G>A | intron_variant | 1 | NM_021167.5 | ENSP00000287957.3 | ||||
GATAD1 | ENST00000644160.1 | n.105+13G>A | intron_variant | |||||||
GATAD1 | ENST00000645746.1 | n.249+13G>A | intron_variant | ENSP00000493785.1 |
Frequencies
GnomAD3 genomes AF: 0.000487 AC: 74AN: 151892Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.00120 AC: 1269AN: 1060574Hom.: 0 Cov.: 31 AF XY: 0.00113 AC XY: 568AN XY: 501120
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GnomAD4 genome AF: 0.000487 AC: 74AN: 152006Hom.: 0 Cov.: 33 AF XY: 0.000390 AC XY: 29AN XY: 74316
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ClinVar
Significance: Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Dilated cardiomyopathy 2B Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 15, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Apr 15, 2022 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Dec 14, 2015 | c.249+13G>A in intron 1 of GATAD1: This variant is not expected to have clinical significance because it is not located within the conserved splice consensus se quence. It has been identified in 1/182 British chromosomes by the 1000 Genomes Project (dbSNP rs548757932). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 10, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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