1-153806936-A-G

Variant names:

• chr1-153806936-A-G
• rs1127091
• NM_020699.4:c.*3241T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_020699.4(GATAD2B):​c.*3241T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 151,944 control chromosomes in the GnomAD database, including 14,562 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 0.42 (14556 hom., cov: 30)
  • Exomes 𝑓: 0.47 (6 hom.)
• Consequence: GATAD2B NM_020699.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.01
• Publications: 19 publications found

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]

GATAD2B Gene-Disease associations (from GenCC):

• severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, G2P, Illumina, Orphanet, Labcorp Genetics (formerly Invitae)

ENSG00000291199 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020699.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATAD2B	NM_020699.4	MANE Select	c.*3241T>C		3_prime_UTR	Exon 11 of 11	NP_065750.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATAD2B	ENST00000368655.5	TSL:1 MANE Select	c.*3241T>C		3_prime_UTR	Exon 11 of 11	ENSP00000357644.4
	GATAD2B	ENST00000637918.1	TSL:5	c.133+4795T>C		intron	N/A	ENSP00000490724.1
	ENSG00000291199	ENST00000820544.1		n.296+12731A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64303 AN: 151790 Hom.: 14547 Cov.: 30

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.445

GnomAD4 exome AF: 0.472 AC: 17 AN: 36 Hom.: 6 Cov.: 0 AF XY: 0.462 AC XY: 12 AN XY: 26

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 14 AN: 28

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 1 AN: 6

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.423 AC: 64327 AN: 151908 Hom.: 14556 Cov.: 30 AF XY: 0.417 AC XY: 30925 AN XY: 74226

African (AFR) AF: 0.290 AC: 12015 AN: 41438

American (AMR) AF: 0.433 AC: 6603 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1996 AN: 3468

East Asian (EAS) AF: 0.150 AC: 775 AN: 5180

South Asian (SAS) AF: 0.356 AC: 1716 AN: 4818

European-Finnish (FIN) AF: 0.434 AC: 4554 AN: 10498

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35145 AN: 67938

Other (OTH) AF: 0.448 AC: 946 AN: 2112

Alfa AF: 0.480 Hom.: 53231

Bravo AF: 0.415

Asia WGS AF: 0.280 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	18
DANN	Benign	0.87
PhyloP100		3.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1127091; hg19: chr1-153779412;