rs12129468

Variant names:

• chr1-153849468-T-A
• rs12129468
• NM_020699.4:c.-1-21120A>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020699.4(GATAD2B):​c.-1-21120A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,132 control chromosomes in the GnomAD database, including 6,681 homozygotes. 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 0.28 (6681 hom., cov: 32)
• Consequence: GATAD2B NM_020699.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATAD2B	NM_020699.4	c.-1-21120A>T		intron_variant	Intron 1 of 10	ENST00000368655.5	NP_065750.1
GATAD2B	XM_047426115.1	c.3-21120A>T		intron_variant	Intron 1 of 10		XP_047282071.1
GATAD2B	XM_047426117.1	c.-1-21120A>T		intron_variant	Intron 1 of 10		XP_047282073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATAD2B	ENST00000368655.5	c.-1-21120A>T		intron_variant	Intron 1 of 10	1	NM_020699.4	ENSP00000357644.4

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42679 AN: 152014 Hom.: 6678 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.0577

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.281 AC: 42694 AN: 152132 Hom.: 6681 Cov.: 32 AF XY: 0.277 AC XY: 20583 AN XY: 74368

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.0574

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.296

Alfa AF: 0.325 Hom.: 1047

Bravo AF: 0.263

Asia WGS AF: 0.204 AC: 711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.62

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

Other links and lift over

dbSNP: rs12129468; hg19: chr1-153821944;