10-8054743-TAAA-TAAAAAA

Variant names:

• chr10-8054743-T-TAAA
• rs60098638
• NM_001002295.2:c.-504_-502dupAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_001002295.2(GATA3):​c.-504_-502dupAAA 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 0.0094 (11 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00941 (1243/132070) while in subpopulation AFR AF= 0.0175 (630/35910). AF 95% confidence interval is 0.0164. There are 11 homozygotes in gnomad4. There are 597 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 1243 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATA3	NM_001002295.2	c.-504_-502dupAAA		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.-504_-502dupAAA		5_prime_UTR_variant	Exon 1 of 6	1	NM_001002295.2	ENSP00000368632.3
GATA3	ENST00000481743.2	c.-369-530_-369-528dupAAA		intron_variant	Intron 1 of 2	2		ENSP00000493486.1
GATA3	ENST00000643001.1	c.-369-530_-369-528dupAAA		intron_variant	Intron 1 of 1			ENSP00000494284.1
GATA3	ENST00000346208.4	c.-518_-517insAAA		upstream_gene_variant		1		ENSP00000341619.3

Frequencies

GnomAD3 genomes AF: 0.00944 AC: 1247 AN: 132084 Hom.: 11 Cov.: 0

Gnomad AFR AF: 0.0176

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00609

Gnomad ASJ AF: 0.00556

Gnomad EAS AF: 0.0120

Gnomad SAS AF: 0.00802

Gnomad FIN AF: 0.00547

Gnomad MID AF: 0.0181

Gnomad NFE AF: 0.00605

Gnomad OTH AF: 0.00898

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.00941 AC: 1243 AN: 132070 Hom.: 11 Cov.: 0 AF XY: 0.00948 AC XY: 597 AN XY: 62966

Gnomad4 AFR AF: 0.0175

Gnomad4 AMR AF: 0.00609

Gnomad4 ASJ AF: 0.00556

Gnomad4 EAS AF: 0.0116

Gnomad4 SAS AF: 0.00783

Gnomad4 FIN AF: 0.00547

Gnomad4 NFE AF: 0.00606

Gnomad4 OTH AF: 0.00895

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;