rs9426935

chr1-153796924-C-T

Variant summary

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

The ENST00000427283.1(ENSG00000231827):n.819+359C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,982 control chromosomes in the GnomAD database, including 13,906 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 0.41 (13906 hom., cov: 32)
• Consequence: ENST00000427283.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.834

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 (NFE) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000427283.1	n.819+359C>T		intron_variant, non_coding_transcript_variant
GATAD2B	ENST00000637918.1	c.136-6848G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62326 AN: 151862 Hom.: 13902 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.0587

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.410 AC: 62342 AN: 151982 Hom.: 13906 Cov.: 32 AF XY: 0.401 AC XY: 29790 AN XY: 74294

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.0584

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.436

Alfa AF: 0.485 Hom.: 8579

Bravo AF: 0.394

Asia WGS AF: 0.236 AC: 819 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	10
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9426935; hg19: chr1-153769400;