rs570613

chr10-8064539-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001002295.2(GATA3):c.924+401C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.602 in 151,978 control chromosomes in the GnomAD database, including 27,668 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 0.60 (27668 hom., cov: 31)
• Consequence: GATA3 NM_001002295.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

Genes affected

GATA3 (HGNC:4172): (GATA binding protein 3) This gene encodes a protein which belongs to the GATA family of transcription factors. The protein contains two GATA-type zinc fingers and is an important regulator of T-cell development and plays an important role in endothelial cell biology. Defects in this gene are the cause of hypoparathyroidism with sensorineural deafness and renal dysplasia. [provided by RefSeq, Nov 2009]

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 (SAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GATA3	NM_001002295.2	c.924+401C>T		intron_variant		ENST00000379328.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GATA3	ENST00000379328.9	c.924+401C>T		intron_variant		1	NM_001002295.2	A1
GATA3	ENST00000346208.4	c.921+401C>T		intron_variant		1		P4
GATA3	ENST00000461472.1	c.444-4934C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91503 AN: 151862 Hom.: 27649 Cov.: 31

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.602 AC: 91564 AN: 151978 Hom.: 27668 Cov.: 31 AF XY: 0.605 AC XY: 44930 AN XY: 74240

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.623

Alfa AF: 0.620 Hom.: 13972

Bravo AF: 0.599

Asia WGS AF: 0.740 AC: 2575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.7
Dann	Benign	0.46

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: rs570613; hg19: chr10-8106502;