GeneBe

ENST00000637918.1:c.134-9795C>A

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_020699.4(GATAD2B):​c.336-1792A>. variant causes a intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 N/A ( N/A hom., cov: )
Exomes 𝑓: N/A ( N/A hom. )

Consequence

GATAD2B
NM_020699.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

No conservation score assigned
Variant links:
Genes affected
GATAD2B (HGNC:30778): (GATA zinc finger domain containing 2B) This gene encodes a zinc finger protein transcriptional repressor. The encoded protein is part of the methyl-CpG-binding protein-1 complex, which represses gene expression by deacetylating methylated nucleosomes. Mutations in this gene are linked to intellectual disability and dysmorphic features associated with cognitive disability. [provided by RefSeq, Jun 2016]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GATAD2BNM_020699.4 linkc.336-1792A>. intron_variant Intron 2 of 10 ENST00000368655.5 NP_065750.1 Q8WXI9
GATAD2BXM_047426115.1 linkc.339-1792A>. intron_variant Intron 2 of 10 XP_047282071.1
GATAD2BXM_047426117.1 linkc.336-1792A>. intron_variant Intron 2 of 10 XP_047282073.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GATAD2BENST00000368655.5 linkc.336-1792A>. intron_variant Intron 2 of 10 1 NM_020699.4 ENSP00000357644.4 Q8WXI9

Frequencies

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-153794003; API