10-8054743-TAAA-TAAAA

Variant names:

• chr10-8054743-T-TA
• rs60098638
• NM_001002295.2:c.-502dupA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001002295.2(GATA3):​c.-502dupA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.10 (2074 hom., cov: 0)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: GATA3 NM_001002295.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.75

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATA3	NM_001002295.2	c.-502dupA		5_prime_UTR_variant	Exon 1 of 6	ENST00000379328.9	NP_001002295.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATA3	ENST00000379328	c.-502dupA		5_prime_UTR_variant	Exon 1 of 6	1	NM_001002295.2	ENSP00000368632.3
GATA3	ENST00000481743.2	c.-369-528dupA		intron_variant	Intron 1 of 2	2		ENSP00000493486.1
GATA3	ENST00000643001.1	c.-369-528dupA		intron_variant	Intron 1 of 1			ENSP00000494284.1
GATA3	ENST00000346208.4	c.-518_-517insA		upstream_gene_variant		1		ENSP00000341619.3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 13770 AN: 132082 Hom.: 2076 Cov.: 0

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.0142

Gnomad AMR AF: 0.0431

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.0169

Gnomad SAS AF: 0.00997

Gnomad FIN AF: 0.0229

Gnomad MID AF: 0.0254

Gnomad NFE AF: 0.00782

Gnomad OTH AF: 0.0685

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.104 AC: 13775 AN: 132068 Hom.: 2074 Cov.: 0 AF XY: 0.103 AC XY: 6496 AN XY: 62954

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.0431

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.0168

Gnomad4 SAS AF: 0.00979

Gnomad4 FIN AF: 0.0229

Gnomad4 NFE AF: 0.00780

Gnomad4 OTH AF: 0.0682

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs60098638; hg19: chr10-8096706;