chr10-8047173-T-G

Position:

• chr10-8047173-T-G

Variant summary

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

The ENST00000643001.1(GATA3):​c.-370+1658T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,086 control chromosomes in the GnomAD database, including 38,826 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 0.71 (38826 hom., cov: 33)
• Consequence: GATA3 ENST00000643001.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GATA3	XM_005252443.6	c.-370+1658T>G		intron_variant			XP_005252500.1
GATA3	XM_047425045.1	c.-370+1658T>G		intron_variant			XP_047281001.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GATA3	ENST00000643001.1	c.-370+1658T>G		intron_variant				ENSP00000494284.1

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107406 AN: 151968 Hom.: 38820 Cov.: 33

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.706 AC: 107437 AN: 152086 Hom.: 38826 Cov.: 33 AF XY: 0.714 AC XY: 53130 AN XY: 74370

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.899

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.733

Alfa AF: 0.744 Hom.: 40216

Bravo AF: 0.705

Asia WGS AF: 0.898 AC: 3116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4143094; hg19: chr10-8089136;