10-8047173-T-G

Variant names:

• chr10-8047173-T-G
• rs4143094
• NM_001441115.1:c.-370+1658T>G

Variant summary

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

The NM_001441115.1(GATA3):​c.-370+1658T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,086 control chromosomes in the GnomAD database, including 38,826 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 0.71 (38826 hom., cov: 33)
• Consequence: GATA3 NM_001441115.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467
• Publications: 30 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001441115.1. 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_001441115.1		c.-370+1658T>G		intron	N/A	NP_001428044.1
	GATA3	NM_001441116.1		c.-370+1232T>G		intron	N/A	NP_001428045.1
	GATA3	NM_001441117.1		c.-712+1658T>G		intron	N/A	NP_001428046.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATA3	ENST00000872595.1		c.-370+1276T>G		intron	N/A	ENSP00000542654.1
	GATA3	ENST00000643001.1		c.-370+1658T>G		intron	N/A	ENSP00000494284.1	A0A2R8Y4T2
	GATA3-AS1	ENST00000831072.1		n.627A>C		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.707 AC: 107406 AN: 151968 Hom.: 38820 Cov.: 33

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.890

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.706 AC: 107437 AN: 152086 Hom.: 38826 Cov.: 33 AF XY: 0.714 AC XY: 53130 AN XY: 74370

African (AFR) AF: 0.544 AC: 22555 AN: 41444

American (AMR) AF: 0.792 AC: 12102 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2698 AN: 3470

East Asian (EAS) AF: 0.943 AC: 4872 AN: 5168

South Asian (SAS) AF: 0.899 AC: 4330 AN: 4816

European-Finnish (FIN) AF: 0.739 AC: 7827 AN: 10590

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50489 AN: 67998

Other (OTH) AF: 0.733 AC: 1547 AN: 2110

Alfa AF: 0.739 Hom.: 109401

Bravo AF: 0.705

Asia WGS AF: 0.898 AC: 3116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.55
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs4143094; hg19: chr10-8089136;