10-8054743-TAAA-TAA

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The NM_001002295.2(GATA3):​c.-502delA 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 0.0078 (6 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
• 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.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00777 (1026/132026) while in subpopulation AFR AF = 0.0177 (634/35914). AF 95% confidence interval is 0.0165. There are 6 homozygotes in GnomAd4. There are 517 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High AC in GnomAd4 at 1026 AD gene.

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.-502delA		5_prime_UTR	Exon 1 of 6	NP_001002295.1	P23771-2
	GATA3	NM_002051.3		c.-502delA		5_prime_UTR	Exon 1 of 6	NP_002042.1	P23771-1
	GATA3	NM_001441131.1		c.-502delA		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.-502delA		5_prime_UTR	Exon 1 of 6	ENSP00000368632.3	P23771-2
	GATA3	ENST00000872595.1		c.-369-528delA		intron	N/A	ENSP00000542654.1
	GATA3	ENST00000481743.2	TSL:2	c.-369-528delA		intron	N/A	ENSP00000493486.1	A0A2R8Y2A9

Frequencies

GnomAD3 genomes AF: 0.00774 AC: 1022 AN: 132038 Hom.: 6 Cov.: 0

Gnomad AFR AF: 0.0176

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00495

Gnomad ASJ AF: 0.00186

Gnomad EAS AF: 0.00178

Gnomad SAS AF: 0.00292

Gnomad FIN AF: 0.0151

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00298

Gnomad OTH AF: 0.0101

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: 0.00777 AC: 1026 AN: 132026 Hom.: 6 Cov.: 0 AF XY: 0.00821 AC XY: 517 AN XY: 62938

African (AFR) AF: 0.0177 AC: 634 AN: 35914

American (AMR) AF: 0.00495 AC: 65 AN: 13134

Ashkenazi Jewish (ASJ) AF: 0.00186 AC: 6 AN: 3234

East Asian (EAS) AF: 0.00179 AC: 8 AN: 4474

South Asian (SAS) AF: 0.00294 AC: 12 AN: 4088

European-Finnish (FIN) AF: 0.0151 AC: 99 AN: 6572

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 256

European-Non Finnish (NFE) AF: 0.00298 AC: 184 AN: 61718

Other (OTH) AF: 0.0101 AC: 18 AN: 1788

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.8
Mutation Taster		=289/11	polymorphism

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;