19-19386860-C-G

Position:

• chr19-19386860-C-G

Variant summary

Our verdict is Benign. Variant got -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

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]

GATAD2A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GATAD2A	NM_001384537.1	c.-7+722C>G		intron_variant			NP_001371466.1
GATAD2A	NM_001300946.3	c.-96+722C>G		intron_variant			NP_001287875.1
GATAD2A	NM_001384511.1	c.-91+722C>G		intron_variant			NP_001371440.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GATAD2A	ENST00000360315.7	c.-7+722C>G		intron_variant		5		ENSP00000353463.3
GATAD2A	ENST00000417582.6	c.-7+722C>G		intron_variant		2		ENSP00000403703.1
GATAD2A	ENST00000494516.6	c.-96+722C>G		intron_variant		2		ENSP00000477171.1
GATAD2A	ENST00000609040.5	n.-2+722C>G		intron_variant		2		ENSP00000476500.1

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

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.644

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.749

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.547

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.8
DANN	Benign	0.46
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

Publications

LitVar

Other links and lift over

dbSNP: rs1858999; hg19: chr19-19497669;