rs10796953

Positions:

• chr1-153795703-A-G
• chr1-153795703-A-T

Variant summary

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

The NR_126565.1(LOC343052):​n.542A>G 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 0.832 in 152,792 control chromosomes in the GnomAD database, including 53,242 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 0.83 (53070 hom., cov: 35)
  • Exomes 𝑓: 0.81 (172 hom.)
• Consequence: LOC343052 NR_126565.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC343052	NR_126565.1	n.542A>G		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000427283.1	n.531A>G		non_coding_transcript_exon_variant	1/11
	ENST00000633218.1	n.542A>G		non_coding_transcript_exon_variant	2/3	3

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126516 AN: 152154 Hom.: 53017 Cov.: 35

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.848

GnomAD4 exome AF: 0.813 AC: 423 AN: 520 Hom.: 172 Cov.: 0 AF XY: 0.805 AC XY: 256 AN XY: 318

Gnomad4 ASJ exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.798

Gnomad4 NFE exome AF: 0.895

Gnomad4 OTH exome AF: 0.875

GnomAD4 genome AF: 0.832 AC: 126630 AN: 152272 Hom.: 53070 Cov.: 35 AF XY: 0.828 AC XY: 61648 AN XY: 74454

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.890

Gnomad4 ASJ AF: 0.907

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.800

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.847

Alfa AF: 0.852 Hom.: 8734

Bravo AF: 0.833

Asia WGS AF: 0.738 AC: 2569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.2
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10796953; hg19: chr1-153768179;