10-8057058-T-C

Position:

• chr10-8057058-T-C

Variant summary

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

The NM_001002295.2(GATA3):​c.241+1162T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 152,082 control chromosomes in the GnomAD database, including 44,554 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 0.75 (44554 hom., cov: 32)
• Consequence: GATA3 NM_001002295.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.532

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=-0.43).
• 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	Protein	UniProt
GATA3	NM_001002295.2	c.241+1162T>C		intron_variant		ENST00000379328.9	NP_001002295.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GATA3	ENST00000379328.9	c.241+1162T>C		intron_variant		1	NM_001002295.2	ENSP00000368632.3
GATA3	ENST00000346208.4	c.241+1162T>C		intron_variant		1		ENSP00000341619.3
GATA3	ENST00000481743.2	c.241+1162T>C		intron_variant		2		ENSP00000493486.1

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114078 AN: 151966 Hom.: 44548 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.750 AC: 114111 AN: 152082 Hom.: 44554 Cov.: 32 AF XY: 0.756 AC XY: 56222 AN XY: 74340

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.906

Gnomad4 EAS AF: 0.955

Gnomad4 SAS AF: 0.930

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.792

Alfa AF: 0.763 Hom.: 6075

Bravo AF: 0.740

Asia WGS AF: 0.906 AC: 3150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	16
DANN	Benign	0.75

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: rs2388486; hg19: chr10-8099021;