dbSNP rs10796953: GATAD2B:c.134-5627T>C (chr1-153795703-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000633218.1(ENSG00000291199):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

ENSG00000291199
ENST00000633218.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.95

Publications

4 publications found

Variant links:

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: G2P, ClinGen, Orphanet, Labcorp Genetics (formerly Invitae), Illumina

GATAD2B links:

ENSG00000231827 (HGNC:):

ENSG00000231827 links:

Genome browser will be placed here

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=-0.78).

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000633218.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC343052	NR_126565.1		n.542A>G		non_coding_transcript_exon	Exon 2 of 3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GATAD2B	ENST00000637918.1	TSL:5	c.134-5627T>C	intron	N/A	ENSP00000490724.1	A0A1B0GW07
ENSG00000231827	ENST00000427283.1	TSL:6	n.531A>G	non_coding_transcript_exon	Exon 1 of 11
ENSG00000291199	ENST00000633218.1	TSL:3	n.542A>G	non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.832

AC:

126516

AN:

152154

Hom.:

53017

Cov.:

show subpopulations

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.:

AF XY:

0.805

AC XY:

256

AN XY:

318

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.798

AC:

343

AN:

430

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.895

AC:

AN:

Other (OTH)

AF:

0.875

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.832

AC:

126630

AN:

152272

Hom.:

53070

Cov.:

AF XY:

0.828

AC XY:

61648

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.764

AC:

31740

AN:

41538

American (AMR)

AF:

0.890

AC:

13618

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.907

AC:

3149

AN:

3470

East Asian (EAS)

AF:

0.569

AC:

2935

AN:

5162

South Asian (SAS)

AF:

0.855

AC:

4133

AN:

4834

European-Finnish (FIN)

AF:

0.800

AC:

8490

AN:

10608

Middle Eastern (MID)

AF:

0.850

AC:

250

AN:

294

European-Non Finnish (NFE)

AF:

0.879

AC:

59810

AN:

68038

Other (OTH)

AF:

0.847

AC:

1792

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1092

2184

3275

4367

5459

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

882

1764

2646

3528

4410

<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:

0.847

Hom.:

10308

Bravo

AF:

0.833

Asia WGS

AF:

0.738

AC:

2569

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

4.2

(source)

DANN

Benign

0.49

PhyloP100

2.0

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over