rs114542403
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_020699.4(GATAD2B):āc.1229C>Gā(p.Ala410Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000292 in 1,613,526 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_020699.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATAD2B | NM_020699.4 | c.1229C>G | p.Ala410Gly | missense_variant | 8/11 | ENST00000368655.5 | |
GATAD2B | XM_047426115.1 | c.1232C>G | p.Ala411Gly | missense_variant | 8/11 | ||
GATAD2B | XM_047426117.1 | c.1229C>G | p.Ala410Gly | missense_variant | 8/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATAD2B | ENST00000368655.5 | c.1229C>G | p.Ala410Gly | missense_variant | 8/11 | 1 | NM_020699.4 | P1 | |
GATAD2B | ENST00000634544.1 | c.1229C>G | p.Ala410Gly | missense_variant | 8/11 | 5 | P1 | ||
GATAD2B | ENST00000634408.1 | c.1181C>G | p.Ala394Gly | missense_variant | 8/11 | 5 | |||
GATAD2B | ENST00000634564.1 | c.485C>G | p.Ala162Gly | missense_variant | 3/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00162 AC: 247AN: 152110Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000370 AC: 93AN: 251108Hom.: 0 AF XY: 0.000273 AC XY: 37AN XY: 135716
GnomAD4 exome AF: 0.000153 AC: 224AN: 1461298Hom.: 1 Cov.: 31 AF XY: 0.000127 AC XY: 92AN XY: 726992
GnomAD4 genome ? AF: 0.00162 AC: 247AN: 152228Hom.: 1 Cov.: 32 AF XY: 0.00152 AC XY: 113AN XY: 74416
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 24, 2020 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 23, 2016 | - - |
Severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at