10-8062759-C-T

Variant names:

• chr10-8062759-C-T
• rs3824660
• NM_001002295.2:c.779-1234C>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.779-1234C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 152,010 control chromosomes in the GnomAD database, including 20,632 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 0.50 (20632 hom., cov: 32)
• Consequence: GATA3 NM_001002295.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.961
• Publications: 30 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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATA3	NM_001002295.2	c.779-1234C>T		intron_variant	Intron 3 of 5	ENST00000379328.9	NP_001002295.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATA3	ENST00000379328.9	c.779-1234C>T		intron_variant	Intron 3 of 5	1	NM_001002295.2	ENSP00000368632.3
GATA3	ENST00000346208.4	c.779-1237C>T		intron_variant	Intron 3 of 5	1		ENSP00000341619.3
GATA3	ENST00000461472.1	c.442+3918C>T		intron_variant	Intron 1 of 2	3		ENSP00000515407.1

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75354 AN: 151892 Hom.: 20624 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.667

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.496 AC: 75368 AN: 152010 Hom.: 20632 Cov.: 32 AF XY: 0.496 AC XY: 36863 AN XY: 74278

African (AFR) AF: 0.239 AC: 9896 AN: 41488

American (AMR) AF: 0.509 AC: 7771 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2059 AN: 3470

East Asian (EAS) AF: 0.653 AC: 3344 AN: 5122

South Asian (SAS) AF: 0.666 AC: 3207 AN: 4818

European-Finnish (FIN) AF: 0.559 AC: 5904 AN: 10560

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.608 AC: 41331 AN: 67960

Other (OTH) AF: 0.536 AC: 1129 AN: 2106

Alfa AF: 0.557 Hom.: 12676

Bravo AF: 0.476

Asia WGS AF: 0.659 AC: 2290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.2
DANN	Benign	0.70
PhyloP100		-0.96
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: rs3824660; hg19: chr10-8104722;