rs3802604

Variant names:

• chr10-8060309-G-A
• rs3802604
• NM_001002295.2:c.778+1468G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-8060309-G-A
• chr10-8060309-G-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.778+1468G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 152,046 control chromosomes in the GnomAD database, including 22,393 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 0.52 (22393 hom., cov: 32)
• Consequence: GATA3 NM_001002295.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94
• Publications: 39 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATA3	NM_001002295.2	c.778+1468G>A		intron_variant	Intron 3 of 5	ENST00000379328.9	NP_001002295.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATA3	ENST00000379328.9	c.778+1468G>A		intron_variant	Intron 3 of 5	1	NM_001002295.2	ENSP00000368632.3
GATA3	ENST00000346208.4	c.778+1468G>A		intron_variant	Intron 3 of 5	1		ENSP00000341619.3
GATA3	ENST00000461472.1	c.442+1468G>A		intron_variant	Intron 1 of 2	3		ENSP00000515407.1

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78619 AN: 151928 Hom.: 22390 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.517 AC: 78624 AN: 152046 Hom.: 22393 Cov.: 32 AF XY: 0.518 AC XY: 38457 AN XY: 74282

African (AFR) AF: 0.254 AC: 10552 AN: 41480

American (AMR) AF: 0.519 AC: 7941 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2092 AN: 3472

East Asian (EAS) AF: 0.651 AC: 3355 AN: 5150

South Asian (SAS) AF: 0.676 AC: 3260 AN: 4820

European-Finnish (FIN) AF: 0.590 AC: 6221 AN: 10548

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43296 AN: 67978

Other (OTH) AF: 0.555 AC: 1170 AN: 2108

Alfa AF: 0.594 Hom.: 90835

Bravo AF: 0.495

Asia WGS AF: 0.661 AC: 2296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	15
DANN	Benign	0.92
PhyloP100		1.9
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: rs3802604; hg19: chr10-8102272;