rs10905284

Variant names:

• chr10-8073399-C-A
• rs10905284
• NM_001002295.2:c.1051-340C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-8073399-C-A
• chr10-8073399-C-G
• chr10-8073399-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001002295.2(GATA3):​c.1051-340C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,930 control chromosomes in the GnomAD database, including 17,890 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 (17890 hom., cov: 31)
• Consequence: GATA3 NM_001002295.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 15 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 Gene-Disease associations (from GenCC):

• hypoparathyroidism-deafness-renal disease syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: PanelApp Australia, G2P, Labcorp Genetics (formerly Invitae), ClinGen, Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATA3	NM_001002295.2	c.1051-340C>A		intron_variant	Intron 5 of 5	ENST00000379328.9	NP_001002295.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATA3	ENST00000379328.9	c.1051-340C>A		intron_variant	Intron 5 of 5	1	NM_001002295.2	ENSP00000368632.3
GATA3	ENST00000346208.4	c.1048-340C>A		intron_variant	Intron 5 of 5	1		ENSP00000341619.3
GATA3	ENST00000461472.1	c.569-340C>A		intron_variant	Intron 2 of 2	3		ENSP00000515407.1

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67883 AN: 151814 Hom.: 17892 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.447 AC: 67890 AN: 151930 Hom.: 17890 Cov.: 31 AF XY: 0.449 AC XY: 33356 AN XY: 74244

African (AFR) AF: 0.150 AC: 6211 AN: 41428

American (AMR) AF: 0.457 AC: 6990 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2049 AN: 3470

East Asian (EAS) AF: 0.555 AC: 2856 AN: 5148

South Asian (SAS) AF: 0.592 AC: 2847 AN: 4806

European-Finnish (FIN) AF: 0.578 AC: 6093 AN: 10542

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.575 AC: 39084 AN: 67938

Other (OTH) AF: 0.495 AC: 1044 AN: 2110

Alfa AF: 0.519 Hom.: 27249

Bravo AF: 0.422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.55
PhyloP100		0.012
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: rs10905284; hg19: chr10-8115362;