rs568727

Variant names:

• chr10-8064738-A-C
• rs568727
• NM_001002295.2:c.924+600A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-8064738-A-C
• chr10-8064738-A-G

Variant summary

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

The NM_001002295.2(GATA3):​c.924+600A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,128 control chromosomes in the GnomAD database, including 26,970 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 0.59 (26970 hom., cov: 34)
• Consequence: GATA3 NM_001002295.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209
• Publications: 8 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: ClinGen, Orphanet, Labcorp Genetics (formerly Invitae), G2P

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.72 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.924+600A>C		intron	N/A	NP_001002295.1	P23771-2
	GATA3	NM_001441115.1		c.924+600A>C		intron	N/A	NP_001428044.1
	GATA3	NM_001441116.1		c.924+600A>C		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.924+600A>C		intron	N/A	ENSP00000368632.3	P23771-2
	GATA3	ENST00000346208.4	TSL:1	c.921+600A>C		intron	N/A	ENSP00000341619.3	P23771-1
	GATA3	ENST00000872595.1		c.924+600A>C		intron	N/A	ENSP00000542654.1

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90178 AN: 152010 Hom.: 26953 Cov.: 34

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.593 AC: 90236 AN: 152128 Hom.: 26970 Cov.: 34 AF XY: 0.596 AC XY: 44350 AN XY: 74368

African (AFR) AF: 0.497 AC: 20630 AN: 41478

American (AMR) AF: 0.634 AC: 9707 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2255 AN: 3470

East Asian (EAS) AF: 0.711 AC: 3684 AN: 5178

South Asian (SAS) AF: 0.740 AC: 3573 AN: 4826

European-Finnish (FIN) AF: 0.583 AC: 6170 AN: 10582

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42167 AN: 67974

Other (OTH) AF: 0.614 AC: 1299 AN: 2114

Alfa AF: 0.610 Hom.: 79185

Bravo AF: 0.588

Asia WGS AF: 0.740 AC: 2573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.39
PhyloP100		0.21
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: rs568727; hg19: chr10-8106701;