rs3824662

chr10-8062245-C-Achr10-8062245-C-Gchr10-8062245-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001002295.2(GATA3):c.779-1748C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 151,898 control chromosomes in the GnomAD database, including 2,831 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.18 (2831 hom., cov: 32)
• Consequence: GATA3 NM_001002295.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.05

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 10-8062245-C-A is Benign according to our data. Variant chr10-8062245-C-A is described in ClinVar as [Benign]. Clinvar id is 1223371.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GATA3	NM_001002295.2	c.779-1748C>A		intron_variant		ENST00000379328.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GATA3	ENST00000379328.9	c.779-1748C>A		intron_variant		1	NM_001002295.2	A1
GATA3	ENST00000346208.4	c.779-1751C>A		intron_variant		1		P4
GATA3	ENST00000461472.1	c.443+3404C>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27039 AN: 151782 Hom.: 2825 Cov.: 32

Gnomad AFR AF: 0.0991

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.178 AC: 27042 AN: 151898 Hom.: 2831 Cov.: 32 AF XY: 0.185 AC XY: 13719 AN XY: 74196

Gnomad4 AFR AF: 0.0990

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.199

Alfa AF: 0.178 Hom.: 3029

Bravo AF: 0.185

Asia WGS AF: 0.206 AC: 712 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 10, 2020

This variant is associated with the following publications: (PMID: 30859636, 23996088, 24141364, 24203929) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.54
Dann	Benign	0.50

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: rs3824662; hg19: chr10-8104208;