19-19386860-C-G

Variant names:

• chr19-19386860-C-G
• rs1858999
• NM_001384537.1:c.-7+722C>G

Variant summary

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

The NM_001384537.1(GATAD2A):​c.-7+722C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 152,026 control chromosomes in the GnomAD database, including 25,068 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 0.56 (25068 hom., cov: 33)
• Consequence: GATAD2A NM_001384537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 11 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001384537.1. 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_001384537.1		c.-7+722C>G		intron	N/A	NP_001371466.1
	GATAD2A	NM_001300946.3		c.-96+722C>G		intron	N/A	NP_001287875.1	Q86YP4-3
	GATAD2A	NM_001384511.1		c.-91+722C>G		intron	N/A	NP_001371440.1	Q86YP4-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATAD2A	ENST00000868304.1		c.-2+722C>G		intron	N/A	ENSP00000538363.1
	GATAD2A	ENST00000868305.1		c.-91+722C>G		intron	N/A	ENSP00000538364.1
	GATAD2A	ENST00000868309.1		c.-304+722C>G		intron	N/A	ENSP00000538368.1

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84796 AN: 151906 Hom.: 25073 Cov.: 33

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.574

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.558 AC: 84789 AN: 152026 Hom.: 25068 Cov.: 33 AF XY: 0.560 AC XY: 41580 AN XY: 74316

African (AFR) AF: 0.369 AC: 15323 AN: 41482

American (AMR) AF: 0.497 AC: 7598 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2232 AN: 3468

East Asian (EAS) AF: 0.694 AC: 3561 AN: 5132

South Asian (SAS) AF: 0.484 AC: 2334 AN: 4820

European-Finnish (FIN) AF: 0.749 AC: 7932 AN: 10596

Middle Eastern (MID) AF: 0.566 AC: 164 AN: 290

European-Non Finnish (NFE) AF: 0.648 AC: 44001 AN: 67924

Other (OTH) AF: 0.547 AC: 1154 AN: 2108

Alfa AF: 0.598 Hom.: 3463

Bravo AF: 0.533

Asia WGS AF: 0.538 AC: 1871 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.8
DANN	Benign	0.46
PhyloP100		-0.82
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs1858999; hg19: chr19-19497669;