chr10-8054743-T-TAA

Variant summary

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

The NM_001002295.2(GATA3):​c.-503_-502dup 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

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 2.75
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GATA3NM_001002295.2 linkuse as main transcriptc.-503_-502dup 5_prime_UTR_variant 1/6 ENST00000379328.9 NP_001002295.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GATA3ENST00000379328.9 linkuse as main transcriptc.-503_-502dup 5_prime_UTR_variant 1/61 NM_001002295.2 ENSP00000368632 A1P23771-2
GATA3ENST00000481743.2 linkuse as main transcriptc.-369-529_-369-528dup intron_variant 2 ENSP00000493486
GATA3ENST00000643001.1 linkuse as main transcriptc.-369-529_-369-528dup intron_variant ENSP00000494284

Frequencies

GnomAD3 genomes
AF:
0.340
AC:
44862
AN:
131820
Hom.:
7548
Cov.:
0
show subpopulations
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
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
AF:
0.340
AC:
44861
AN:
131808
Hom.:
7553
Cov.:
0
AF XY:
0.339
AC XY:
21271
AN XY:
62820
show subpopulations
Gnomad4 AFR
AF:
0.253
Gnomad4 AMR
AF:
0.359
Gnomad4 ASJ
AF:
0.390
Gnomad4 EAS
AF:
0.433
Gnomad4 SAS
AF:
0.447
Gnomad4 FIN
AF:
0.281
Gnomad4 NFE
AF:
0.374
Gnomad4 OTH
AF:
0.351

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Hypoparathyroidism, deafness, renal disease syndrome Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs60098638; hg19: chr10-8096706; API