19-19499787-C-T

Variant names:

• chr19-19499787-C-T
• rs3794991
• NM_001384528.1:c.1204+1065C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001384528.1(GATAD2A):​c.1204+1065C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0746 in 152,032 control chromosomes in the GnomAD database, including 441 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 0.075 (441 hom., cov: 33)
• Consequence: GATAD2A NM_001384528.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904
• Publications: 34 publications found

Genes affected

GATAD2A (HGNC:29989): (GATA zinc finger domain containing 2A) Enables protein-macromolecule adaptor activity. Involved in negative regulation of transcription, DNA-templated. Located in nucleoplasm. Part of NuRD complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001384528.1. 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
	GATAD2A	NM_001384528.1	MANE Select	c.1204+1065C>T		intron	N/A	NP_001371457.1	Q86YP4-3
	GATAD2A	NM_001384537.1		c.1205-339C>T		intron	N/A	NP_001371466.1
	GATAD2A	NM_001300946.3		c.1204+1065C>T		intron	N/A	NP_001287875.1	Q86YP4-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATAD2A	ENST00000683918.1	MANE Select	c.1204+1065C>T		intron	N/A	ENSP00000508398.1	Q86YP4-3
	GATAD2A	ENST00000358713.7	TSL:1	c.1204+1065C>T		intron	N/A	ENSP00000351552.3	Q86YP4-1
	GATAD2A	ENST00000915070.1		c.1205-306C>T		intron	N/A	ENSP00000585129.1

Frequencies

GnomAD3 genomes AF: 0.0745 AC: 11323 AN: 151914 Hom.: 434 Cov.: 33

Gnomad AFR AF: 0.0656

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0643

Gnomad ASJ AF: 0.0513

Gnomad EAS AF: 0.0895

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0621

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.0648

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

GnomAD4 genome AF: 0.0746 AC: 11343 AN: 152032 Hom.: 441 Cov.: 33 AF XY: 0.0751 AC XY: 5582 AN XY: 74332

African (AFR) AF: 0.0656 AC: 2722 AN: 41522

American (AMR) AF: 0.0642 AC: 982 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0513 AC: 178 AN: 3470

East Asian (EAS) AF: 0.0893 AC: 462 AN: 5172

South Asian (SAS) AF: 0.111 AC: 534 AN: 4824

European-Finnish (FIN) AF: 0.0621 AC: 656 AN: 10566

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0815 AC: 5529 AN: 67872

Other (OTH) AF: 0.0727 AC: 153 AN: 2104

Alfa AF: 0.0703 Hom.: 84

Bravo AF: 0.0736

Asia WGS AF: 0.153 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.59
PhyloP100		-0.90
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs3794991; hg19: chr19-19610596;