10-8054236-A-G

Variant names:

• chr10-8054236-A-G
• rs1269486
• ENST00000831073.1:n.137T>C

Variant summary

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

The ENST00000831073.1(GATA3-AS1):​n.137T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,152 control chromosomes in the GnomAD database, including 45,426 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 0.77 (45426 hom., cov: 33)
• Consequence: GATA3-AS1 ENST00000831073.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 18 publications found

Genes affected

GATA3-AS1 (HGNC:33786): (GATA3 antisense RNA 1)

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000831073.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATA3	NM_001441115.1		c.-369-1051A>G		intron	N/A	NP_001428044.1
	GATA3	NM_001441116.1		c.-369-1051A>G		intron	N/A	NP_001428045.1
	GATA3	NM_001441117.1		c.-369-1051A>G		intron	N/A	NP_001428046.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATA3-AS1	ENST00000831073.1		n.137T>C		non_coding_transcript_exon	Exon 1 of 2
	GATA3-AS1	ENST00000831074.1		n.130T>C		non_coding_transcript_exon	Exon 1 of 2
	GATA3-AS1	ENST00000831079.1		n.130T>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117345 AN: 152034 Hom.: 45411 Cov.: 33

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.772 AC: 117403 AN: 152152 Hom.: 45426 Cov.: 33 AF XY: 0.776 AC XY: 57735 AN XY: 74378

African (AFR) AF: 0.772 AC: 32047 AN: 41496

American (AMR) AF: 0.811 AC: 12398 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2801 AN: 3466

East Asian (EAS) AF: 0.954 AC: 4938 AN: 5174

South Asian (SAS) AF: 0.903 AC: 4360 AN: 4828

European-Finnish (FIN) AF: 0.742 AC: 7863 AN: 10592

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50331 AN: 67980

Other (OTH) AF: 0.777 AC: 1642 AN: 2114

Alfa AF: 0.757 Hom.: 7218

Bravo AF: 0.778

Asia WGS AF: 0.909 AC: 3159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.7
DANN	Benign	0.33
PhyloP100		-0.15
PromoterAI		-0.011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1269486; hg19: chr10-8096199;