chr19-19386860-C-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001384537.1(GATAD2A):​c.-7+722C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

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>A		intron	N/A	NP_001371466.1
	GATAD2A	NM_001300946.3		c.-96+722C>A		intron	N/A	NP_001287875.1	Q86YP4-3
	GATAD2A	NM_001384511.1		c.-91+722C>A		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>A		intron	N/A	ENSP00000538363.1
	GATAD2A	ENST00000868305.1		c.-91+722C>A		intron	N/A	ENSP00000538364.1
	GATAD2A	ENST00000868309.1		c.-304+722C>A		intron	N/A	ENSP00000538368.1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.7
DANN	Benign	0.44
PhyloP100		-0.82
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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;