rs3781093

Positions:

• chr10-8059964-T-C

Variant summary

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

The NM_001002295.2(GATA3):​c.778+1123T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,096 control chromosomes in the GnomAD database, including 3,087 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 0.19 (3087 hom., cov: 33)
• Consequence: GATA3 NM_001002295.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.464

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GATA3	NM_001002295.2	c.778+1123T>C		intron_variant		ENST00000379328.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GATA3	ENST00000379328.9	c.778+1123T>C		intron_variant		1	NM_001002295.2	A1
GATA3	ENST00000346208.4	c.778+1123T>C		intron_variant		1		P4
GATA3	ENST00000461472.1	c.443+1123T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29376 AN: 151978 Hom.: 3080 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.193 AC: 29396 AN: 152096 Hom.: 3087 Cov.: 33 AF XY: 0.199 AC XY: 14792 AN XY: 74348

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.196

Alfa AF: 0.172 Hom.: 1512

Bravo AF: 0.206

Asia WGS AF: 0.213 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.2
DANN	Benign	0.48

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: rs3781093; hg19: chr10-8101927; COSMIC: COSV60522152; COSMIC: COSV60522152;