rs11583896

Positions:

• chr1-153796506-G-A

Variant summary

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

The ENST00000427283.1(ENSG00000231827):​n.760G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,294 control chromosomes in the GnomAD database, including 5,939 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 0.26 (5933 hom., cov: 33)
  • Exomes 𝑓: 0.25 (6 hom.)
• Consequence: ENST00000427283.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

Genes affected

(HGNC:):

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000427283.1	n.760G>A		non_coding_transcript_exon_variant	3/11
GATAD2B	ENST00000637918.1	c.136-6430C>T		intron_variant		5		ENSP00000490724

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40194 AN: 152038 Hom.: 5933 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.290

GnomAD4 exome AF: 0.246 AC: 34 AN: 138 Hom.: 6 Cov.: 0 AF XY: 0.207 AC XY: 19 AN XY: 92

Gnomad4 AFR exome AF: 0.250

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.219

Gnomad4 NFE exome AF: 0.244

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.264 AC: 40205 AN: 152156 Hom.: 5933 Cov.: 33 AF XY: 0.268 AC XY: 19911 AN XY: 74362

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.286

Alfa AF: 0.298 Hom.: 4053

Bravo AF: 0.267

Asia WGS AF: 0.277 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.93
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11583896; hg19: chr1-153768982;