7-92456449-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_021167.5(GATAD1):c.697C>T(p.Arg233Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0147 in 1,611,378 control chromosomes in the GnomAD database, including 234 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R233Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_021167.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATAD1 | NM_021167.5 | c.697C>T | p.Arg233Trp | missense_variant | 5/5 | ENST00000287957.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATAD1 | ENST00000287957.5 | c.697C>T | p.Arg233Trp | missense_variant | 5/5 | 1 | NM_021167.5 | P1 | |
GATAD1 | ENST00000493878.1 | n.1305C>T | non_coding_transcript_exon_variant | 3/3 | 1 | ||||
GATAD1 | ENST00000465247.1 | n.709C>T | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
GATAD1 | ENST00000645746.1 | c.*288C>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/6 |
Frequencies
GnomAD3 genomes AF: 0.0100 AC: 1525AN: 152204Hom.: 15 Cov.: 32
GnomAD3 exomes AF: 0.0109 AC: 2734AN: 251366Hom.: 16 AF XY: 0.0114 AC XY: 1542AN XY: 135854
GnomAD4 exome AF: 0.0152 AC: 22210AN: 1459056Hom.: 218 Cov.: 29 AF XY: 0.0152 AC XY: 11048AN XY: 725958
GnomAD4 genome AF: 0.0100 AC: 1525AN: 152322Hom.: 16 Cov.: 32 AF XY: 0.00975 AC XY: 726AN XY: 74484
ClinVar
Submissions by phenotype
not specified Benign:4
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 17, 2014 | 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. - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 19, 2012 | p.Arg233Trp in Exon 05 of GATAD1: This variant is not expected to have clinical significance because it has been identified in 1.5% (107/7020) of European Ameri can chromosomes from a broad population by the NHLBI Exome Sequencing Project (h ttp://evs.gs.washington.edu/EVS; dbSNP rs34768413). - |
Dilated cardiomyopathy 2B Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 06, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Hypertrophic cardiomyopathy 2 Benign:1
Likely benign, no assertion criteria provided | clinical testing | Institute of Human Genetics, University of Wuerzburg | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at