rs570613

Variant names:

• chr10-8064539-C-T
• rs570613
• NM_001002295.2:c.924+401C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

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]

GATA3 Gene-Disease associations (from GenCC):

• hypoparathyroidism-deafness-renal disease syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: PanelApp Australia, G2P, Labcorp Genetics (formerly Invitae), ClinGen, Orphanet

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATA3	NM_001002295.2	c.924+401C>T		intron_variant	Intron 4 of 5	ENST00000379328.9	NP_001002295.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATA3	ENST00000379328.9	c.924+401C>T		intron_variant	Intron 4 of 5	1	NM_001002295.2	ENSP00000368632.3
GATA3	ENST00000346208.4	c.921+401C>T		intron_variant	Intron 4 of 5	1		ENSP00000341619.3
GATA3	ENST00000461472.1	c.443-4934C>T		intron_variant	Intron 1 of 2	3		ENSP00000515407.1

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

African (AFR) AF: 0.530 AC: 21955 AN: 41432

American (AMR) AF: 0.637 AC: 9744 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2257 AN: 3472

East Asian (EAS) AF: 0.713 AC: 3676 AN: 5158

South Asian (SAS) AF: 0.741 AC: 3565 AN: 4812

European-Finnish (FIN) AF: 0.584 AC: 6147 AN: 10530

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42153 AN: 67972

Other (OTH) AF: 0.623 AC: 1315 AN: 2110

Alfa AF: 0.618 Hom.: 15561

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
PhyloP100		0.027
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: rs570613; hg19: chr10-8106502;