NM_001002295.2:c.-504_-502dupAAA

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• 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 = 0.00941 (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 the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High AC in GnomAd4 at 1243 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.-504_-502dupAAA		5_prime_UTR	Exon 1 of 6	NP_001002295.1	P23771-2
	GATA3	NM_002051.3		c.-504_-502dupAAA		5_prime_UTR	Exon 1 of 6	NP_002042.1	P23771-1
	GATA3	NM_001441131.1		c.-504_-502dupAAA		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.-504_-502dupAAA		5_prime_UTR	Exon 1 of 6	ENSP00000368632.3	P23771-2
	GATA3	ENST00000872595.1		c.-369-530_-369-528dupAAA		intron	N/A	ENSP00000542654.1
	GATA3	ENST00000481743.2	TSL:2	c.-369-530_-369-528dupAAA		intron	N/A	ENSP00000493486.1	A0A2R8Y2A9

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

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

African (AFR) AF: 0.0175 AC: 630 AN: 35910

American (AMR) AF: 0.00609 AC: 80 AN: 13134

Ashkenazi Jewish (ASJ) AF: 0.00556 AC: 18 AN: 3238

East Asian (EAS) AF: 0.0116 AC: 52 AN: 4472

South Asian (SAS) AF: 0.00783 AC: 32 AN: 4088

European-Finnish (FIN) AF: 0.00547 AC: 36 AN: 6576

Middle Eastern (MID) AF: 0.0195 AC: 5 AN: 256

European-Non Finnish (NFE) AF: 0.00606 AC: 374 AN: 61760

Other (OTH) AF: 0.00895 AC: 16 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		=300/0	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; COSMIC: COSV60522006;