chr10-8053377-G-A

Position:

• chr10-8053377-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_005252442.3(GATA3):​c.-771G>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 152,110 control chromosomes in the GnomAD database, including 17,256 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.45 (17253 hom., cov: 32)
  • Exomes 𝑓: 0.50 (3 hom.)
• Consequence: GATA3 XM_005252442.3 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254

Genes affected

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

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GATA3	XM_005252442.3	c.-771G>A		5_prime_UTR_premature_start_codon_gain_variant	2/7		XP_005252499.1
GATA3	XM_047425044.1	c.-771G>A		5_prime_UTR_premature_start_codon_gain_variant	2/7		XP_047281000.1
GATA3	XM_005252442.3	c.-771G>A		5_prime_UTR_variant	2/7		XP_005252499.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GATA3-AS1	ENST00000458727.1	n.73C>T		non_coding_transcript_exon_variant	1/2	1
GATA3	ENST00000643001.1	c.-369-1910G>A		intron_variant				ENSP00000494284.1
GATA3-AS1	ENST00000355358.1	n.108C>T		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68542 AN: 151976 Hom.: 17247 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.487

GnomAD4 exome AF: 0.500 AC: 8 AN: 16 Hom.: 3 Cov.: 0 AF XY: 0.500 AC XY: 4 AN XY: 8

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.429

GnomAD4 genome AF: 0.451 AC: 68549 AN: 152094 Hom.: 17253 Cov.: 32 AF XY: 0.452 AC XY: 33629 AN XY: 74352

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.492

Alfa AF: 0.497 Hom.: 8126

Bravo AF: 0.433

Asia WGS AF: 0.644 AC: 2239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2275806; hg19: chr10-8095340;