10-8054906-CTTT-CT

Variant names:

• chr10-8054906-CTT-C
• rs397846644
• NM_001002295.2:c.-370+27_-370+28delTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_001002295.2(GATA3):​c.-370+27_-370+28delTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 146,314 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000055 (0 hom., cov: 24)
  • Exomes 𝑓: 0.0069 (0 hom.)
• Consequence: GATA3 NM_001002295.2 intron
• Clinical Significance: Not reported in ClinVar
• 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 -8 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.0069 (7/1014) while in subpopulation SAS AF= 0.0556 (1/18). AF 95% confidence interval is 0.0014. There are 0 homozygotes in gnomad4_exome. There are 4 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 8 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATA3	NM_001002295.2	c.-370+27_-370+28delTT		intron_variant	Intron 1 of 5	ENST00000379328.9	NP_001002295.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATA3	ENST00000379328.9	c.-370+16_-370+17delTT		intron_variant	Intron 1 of 5	1	NM_001002295.2	ENSP00000368632.3
GATA3	ENST00000346208.4	c.-370+16_-370+17delTT		intron_variant	Intron 1 of 5	1		ENSP00000341619.3
GATA3	ENST00000481743.2	c.-369-380_-369-379delTT		intron_variant	Intron 1 of 2	2		ENSP00000493486.1
GATA3	ENST00000643001.1	c.-369-380_-369-379delTT		intron_variant	Intron 1 of 1			ENSP00000494284.1

Frequencies

GnomAD3 genomes AF: 0.0000551 AC: 8 AN: 145300 Hom.: 0 Cov.: 24

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000297

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000552

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000152

Gnomad OTH AF: 0.000512

GnomAD4 exome AF: 0.00690 AC: 7 AN: 1014 Hom.: 0 AF XY: 0.00755 AC XY: 4 AN XY: 530

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0278

Gnomad4 ASJ exome AF: 0.0244

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0556

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00515

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000551 AC: 8 AN: 145300 Hom.: 0 Cov.: 24 AF XY: 0.0000425 AC XY: 3 AN XY: 70608

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.000297

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000552

Gnomad4 NFE AF: 0.0000152

Gnomad4 OTH AF: 0.000512

ClinVar

Not reported in ClinVar

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;