1-153806760-C-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000368655.5(GATAD2B):​c.*3417G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000046 ( 0 hom., cov: 26)
Failed GnomAD Quality Control

Consequence

GATAD2B
ENST00000368655.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0690
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 Likely_benign. Variant got -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GATAD2BNM_020699.4 linkuse as main transcriptc.*3417G>C 3_prime_UTR_variant 11/11 ENST00000368655.5 NP_065750.1
GATAD2BXM_047426115.1 linkuse as main transcriptc.*3417G>C 3_prime_UTR_variant 11/11 XP_047282071.1
GATAD2BXM_047426117.1 linkuse as main transcriptc.*3417G>C 3_prime_UTR_variant 11/11 XP_047282073.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GATAD2BENST00000368655.5 linkuse as main transcriptc.*3417G>C 3_prime_UTR_variant 11/111 NM_020699.4 ENSP00000357644 P1
GATAD2BENST00000637918.1 linkuse as main transcriptc.135+4971G>C intron_variant 5 ENSP00000490724

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
6
AN:
130286
Hom.:
0
Cov.:
26
FAILED QC
Gnomad AFR
AF:
0.0000297
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000844
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000361
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000163
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000461
AC:
6
AN:
130286
Hom.:
0
Cov.:
26
AF XY:
0.0000802
AC XY:
5
AN XY:
62380
show subpopulations
Gnomad4 AFR
AF:
0.0000297
Gnomad4 AMR
AF:
0.0000844
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000361
Gnomad4 NFE
AF:
0.0000163
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.91
DANN
Benign
0.56

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1127092; hg19: chr1-153779236; API