rs528778

Variant names:

• chr10-8070180-T-C
• rs528778
• NM_001002295.2:c.1050+582T>C

Your query was ambiguous. Multiple possible variants found:

• chr10-8070180-T-C
• chr10-8070180-T-G

Variant summary

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

The NM_001002295.2(GATA3):​c.1050+582T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,184 control chromosomes in the GnomAD database, including 50,073 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 0.81 (50073 hom., cov: 31)
• Consequence: GATA3 NM_001002295.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304
• Publications: 8 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001002295.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATA3	NM_001002295.2	MANE Select	c.1050+582T>C		intron	N/A	NP_001002295.1
	GATA3	NM_001441115.1		c.1050+582T>C		intron	N/A	NP_001428044.1
	GATA3	NM_001441116.1		c.1050+582T>C		intron	N/A	NP_001428045.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATA3	ENST00000379328.9	TSL:1 MANE Select	c.1050+582T>C		intron	N/A	ENSP00000368632.3
	GATA3	ENST00000346208.4	TSL:1	c.1047+582T>C		intron	N/A	ENSP00000341619.3
	GATA3	ENST00000872595.1		c.1050+582T>C		intron	N/A	ENSP00000542654.1

Frequencies

GnomAD3 genomes AF: 0.810 AC: 123242 AN: 152066 Hom.: 50027 Cov.: 31

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.811 AC: 123346 AN: 152184 Hom.: 50073 Cov.: 31 AF XY: 0.815 AC XY: 60652 AN XY: 74408

African (AFR) AF: 0.790 AC: 32779 AN: 41500

American (AMR) AF: 0.849 AC: 12991 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3129 AN: 3472

East Asian (EAS) AF: 0.953 AC: 4933 AN: 5174

South Asian (SAS) AF: 0.912 AC: 4396 AN: 4818

European-Finnish (FIN) AF: 0.825 AC: 8741 AN: 10592

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.788 AC: 53584 AN: 68010

Other (OTH) AF: 0.820 AC: 1736 AN: 2116

Alfa AF: 0.795 Hom.: 21537

Bravo AF: 0.814

Asia WGS AF: 0.919 AC: 3196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.30
PhyloP100		0.30
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: rs528778; hg19: chr10-8112143;