10-8054236-A-G

Position:

• chr10-8054236-A-G

Variant summary

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

The ENST00000481743.2(GATA3):​c.-370+458A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,152 control chromosomes in the GnomAD database, including 45,426 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 0.77 (45426 hom., cov: 33)
• Consequence: GATA3 ENST00000481743.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GATA3	XM_005252442.3	c.-370+458A>G		intron_variant			XP_005252499.1
GATA3	XM_005252443.6	c.-369-1051A>G		intron_variant			XP_005252500.1
GATA3	XM_047425044.1	c.-370+458A>G		intron_variant			XP_047281000.1
GATA3	XM_047425045.1	c.-369-1051A>G		intron_variant			XP_047281001.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GATA3	ENST00000481743.2	c.-370+458A>G		intron_variant		2		ENSP00000493486
GATA3	ENST00000643001.1	c.-369-1051A>G		intron_variant				ENSP00000494284

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117345 AN: 152034 Hom.: 45411 Cov.: 33

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.772 AC: 117403 AN: 152152 Hom.: 45426 Cov.: 33 AF XY: 0.776 AC XY: 57735 AN XY: 74378

Gnomad4 AFR AF: 0.772

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.777

Alfa AF: 0.756 Hom.: 6982

Bravo AF: 0.778

Asia WGS AF: 0.909 AC: 3159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.7
DANN	Benign	0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1269486; hg19: chr10-8096199;