dbSNP rs11583896: ENSG00000231827:n.760G>A (chr1-153796506-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

ENSG00000231827
ENST00000427283.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.07

Publications

20 publications found

Variant links:

Genes affected

ENSG00000231827 (HGNC:):

ENSG00000231827 links:

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)

GATAD2B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC343052	NR_126565.1 link	n.*204G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
ENSG00000231827	ENST00000427283.1 link	n.760G>A	non_coding_transcript_exon_variant	Exon 3 of 11	6
GATAD2B	ENST00000637918.1 link	c.134-6430C>T	intron_variant	Intron 2 of 3	5	ENSP00000490724.1	A0A1B0GW07
ENSG00000291199	ENST00000820544.1 link	n.296+2301G>A	intron_variant	Intron 1 of 1
ENSG00000291199	ENST00000633218.1 link	n.*204G>A	downstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.264

AC:

40194

AN:

152038

Hom.:

5933

Cov.:

show subpopulations

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:

AN:

138

Hom.:

Cov.:

AF XY:

0.207

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.250

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.219

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.244

AC:

AN:

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.264

AC:

40205

AN:

152156

Hom.:

5933

Cov.:

AF XY:

0.268

AC XY:

19911

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.125

AC:

5206

AN:

41554

American (AMR)

AF:

0.384

AC:

5882

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.299

AC:

1037

AN:

3470

East Asian (EAS)

AF:

0.276

AC:

1430

AN:

5176

South Asian (SAS)

AF:

0.323

AC:

1554

AN:

4812

European-Finnish (FIN)

AF:

0.310

AC:

3281

AN:

10568

Middle Eastern (MID)

AF:

0.316

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.308

AC:

20911

AN:

67956

Other (OTH)

AF:

0.286

AC:

606

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1490

2980

4469

5959

7449

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

416

832

1248

1664

2080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.295

Hom.:

5454

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

(source)

DANN

Benign

0.38

PhyloP100

1.1

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over