10-8057214-C-T

Variant names:

• chr10-8057214-C-T
• rs369421
• NM_001002295.2:c.242-1091C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001002295.2(GATA3):​c.242-1091C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 152,196 control chromosomes in the GnomAD database, including 55,702 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 0.86 (55702 hom., cov: 33)
• Consequence: GATA3 NM_001002295.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348
• Publications: 9 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

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.242-1091C>T		intron	N/A	NP_001002295.1	P23771-2
	GATA3	NM_001441115.1		c.242-1091C>T		intron	N/A	NP_001428044.1
	GATA3	NM_001441116.1		c.242-1091C>T		intron	N/A	NP_001428045.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATA3	ENST00000379328.9	TSL:1 MANE Select	c.242-1091C>T		intron	N/A	ENSP00000368632.3	P23771-2
	GATA3	ENST00000346208.4	TSL:1	c.242-1091C>T		intron	N/A	ENSP00000341619.3	P23771-1
	GATA3	ENST00000872595.1		c.242-1091C>T		intron	N/A	ENSP00000542654.1

Frequencies

GnomAD3 genomes AF: 0.855 AC: 130064 AN: 152078 Hom.: 55664 Cov.: 33

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.871

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.857

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.854

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.855 AC: 130160 AN: 152196 Hom.: 55702 Cov.: 33 AF XY: 0.858 AC XY: 63803 AN XY: 74398

African (AFR) AF: 0.875 AC: 36330 AN: 41528

American (AMR) AF: 0.871 AC: 13320 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3146 AN: 3472

East Asian (EAS) AF: 0.956 AC: 4954 AN: 5184

South Asian (SAS) AF: 0.932 AC: 4491 AN: 4820

European-Finnish (FIN) AF: 0.832 AC: 8794 AN: 10568

Middle Eastern (MID) AF: 0.853 AC: 249 AN: 292

European-Non Finnish (NFE) AF: 0.827 AC: 56232 AN: 68010

Other (OTH) AF: 0.855 AC: 1810 AN: 2116

Alfa AF: 0.852 Hom.: 37446

Bravo AF: 0.858

Asia WGS AF: 0.933 AC: 3241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	10
DANN	Benign	0.80
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs369421; hg19: chr10-8099177;