chr10-8054906-CT-C

Position:

• chr10-8054906-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001002295.2(GATA3):​c.-370+28del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0797 in 146,080 control chromosomes in the GnomAD database, including 472 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.079 (469 hom., cov: 24)
  • Exomes 𝑓: 0.16 (3 hom.)
• Consequence: GATA3 NM_001002295.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.19

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 10-8054906-CT-C is Benign according to our data. Variant chr10-8054906-CT-C is described in ClinVar as [Benign]. Clinvar id is 301103.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-8054906-CT-C is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GATA3	NM_001002295.2	c.-370+28del		intron_variant		ENST00000379328.9	NP_001002295.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GATA3	ENST00000379328.9	c.-370+28del		intron_variant		1	NM_001002295.2	ENSP00000368632	A1
GATA3	ENST00000346208.4	c.-370+28del		intron_variant		1		ENSP00000341619	P4
GATA3	ENST00000481743.2	c.-369-368del		intron_variant		2		ENSP00000493486
GATA3	ENST00000643001.1	c.-369-368del		intron_variant				ENSP00000494284

Frequencies

GnomAD3 genomes AF: 0.0791 AC: 11476 AN: 145044 Hom.: 467 Cov.: 24

Gnomad AFR AF: 0.0672

Gnomad AMI AF: 0.0257

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.0657

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.0459

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0662

Gnomad NFE AF: 0.0901

Gnomad OTH AF: 0.0850

GnomAD4 exome AF: 0.157 AC: 157 AN: 1000 Hom.: 3 Cov.: 0 AF XY: 0.138 AC XY: 72 AN XY: 522

Gnomad4 AFR exome AF: 0.150

Gnomad4 AMR exome AF: 0.0833

Gnomad4 ASJ exome AF: 0.0875

Gnomad4 EAS exome AF: 0.154

Gnomad4 SAS exome AF: 0.100

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.185

Gnomad4 OTH exome AF: 0.0854

GnomAD4 genome AF: 0.0792 AC: 11490 AN: 145080 Hom.: 469 Cov.: 24 AF XY: 0.0784 AC XY: 5529 AN XY: 70524

Gnomad4 AFR AF: 0.0674

Gnomad4 AMR AF: 0.0596

Gnomad4 ASJ AF: 0.0657

Gnomad4 EAS AF: 0.0265

Gnomad4 SAS AF: 0.0462

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.0902

Gnomad4 OTH AF: 0.0845

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hypoparathyroidism, deafness, renal disease syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs397846644; hg19: chr10-8096869;