10-8057214-C-T

Position:

• chr10-8057214-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001002295.2(GATA3):​c.242-1091C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 152,196 control chromosomes in the GnomAD database, including 55,702 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 0.86 (55702 hom., cov: 33)
• Consequence: GATA3 NM_001002295.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GATA3	NM_001002295.2	c.242-1091C>T		intron_variant		ENST00000379328.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GATA3	ENST00000379328.9	c.242-1091C>T		intron_variant		1	NM_001002295.2	A1
GATA3	ENST00000346208.4	c.242-1091C>T		intron_variant		1		P4
GATA3	ENST00000481743.2	c.242-1091C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.855 AC: 130064 AN: 152078 Hom.: 55664 Cov.: 33

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.857

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.855 AC: 130160 AN: 152196 Hom.: 55702 Cov.: 33 AF XY: 0.858 AC XY: 63803 AN XY: 74398

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.871

Gnomad4 ASJ AF: 0.906

Gnomad4 EAS AF: 0.956

Gnomad4 SAS AF: 0.932

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.855

Alfa AF: 0.838 Hom.: 13746

Bravo AF: 0.858

Asia WGS AF: 0.933 AC: 3241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	10
DANN	Benign	0.80

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: rs369421; hg19: chr10-8099177;