10-8054743-T-TAA

Variant names:

• chr10-8054743-T-TAA
• rs60098638
• NM_001002295.2:c.-503_-502dupAA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001002295.2(GATA3):​c.-503_-502dupAA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★★).

• Frequency:
  • Genomes: 𝑓 0.34 (7553 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GATA3 NM_001002295.2 5_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:2
• Conservation: PhyloP100: 2.75
• Publications: 0 publications found

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]

GATA3-AS1 (HGNC:33786): (GATA3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001002295.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATA3	NM_001002295.2	MANE Select	c.-503_-502dupAA		5_prime_UTR	Exon 1 of 6	NP_001002295.1	P23771-2
	GATA3	NM_002051.3		c.-503_-502dupAA		5_prime_UTR	Exon 1 of 6	NP_002042.1	P23771-1
	GATA3	NM_001441131.1		c.-503_-502dupAA		5_prime_UTR	Exon 1 of 6	NP_001428060.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATA3	ENST00000379328.9	TSL:1 MANE Select	c.-503_-502dupAA		5_prime_UTR	Exon 1 of 6	ENSP00000368632.3	P23771-2
	GATA3	ENST00000872595.1		c.-369-529_-369-528dupAA		intron	N/A	ENSP00000542654.1
	GATA3	ENST00000481743.2	TSL:2	c.-369-529_-369-528dupAA		intron	N/A	ENSP00000493486.1	A0A2R8Y2A9

Frequencies

GnomAD3 genomes AF: 0.340 AC: 44862 AN: 131820 Hom.: 7548 Cov.: 0

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.349

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.346

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.340 AC: 44861 AN: 131808 Hom.: 7553 Cov.: 0 AF XY: 0.339 AC XY: 21271 AN XY: 62820

African (AFR) AF: 0.253 AC: 9053 AN: 35846

American (AMR) AF: 0.359 AC: 4708 AN: 13098

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1264 AN: 3238

East Asian (EAS) AF: 0.433 AC: 1929 AN: 4454

South Asian (SAS) AF: 0.447 AC: 1822 AN: 4078

European-Finnish (FIN) AF: 0.281 AC: 1845 AN: 6560

Middle Eastern (MID) AF: 0.368 AC: 95 AN: 258

European-Non Finnish (NFE) AF: 0.374 AC: 23087 AN: 61648

Other (OTH) AF: 0.351 AC: 627 AN: 1786

Alfa AF: 0.00 Hom.: 0

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	1	-	Hypoparathyroidism, deafness, renal disease syndrome (1)
-	1	-	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.8
Mutation Taster		=300/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs60098638; hg19: chr10-8096706;