NM_001002295.2:c.241+1162T>C

Variant names:

• chr10-8057058-T-C
• rs2388486
• NM_001002295.2:c.241+1162T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001002295.2(GATA3):​c.241+1162T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 152,082 control chromosomes in the GnomAD database, including 44,554 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 0.75 (44554 hom., cov: 32)
• Consequence: GATA3 NM_001002295.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.532
• 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-AS1 (HGNC:33786): (GATA3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATA3	NM_001002295.2	c.241+1162T>C		intron_variant	Intron 2 of 5	ENST00000379328.9	NP_001002295.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATA3	ENST00000379328.9	c.241+1162T>C		intron_variant	Intron 2 of 5	1	NM_001002295.2	ENSP00000368632.3
GATA3	ENST00000346208.4	c.241+1162T>C		intron_variant	Intron 2 of 5	1		ENSP00000341619.3
GATA3	ENST00000481743.2	c.241+1162T>C		intron_variant	Intron 2 of 2	2		ENSP00000493486.1
GATA3-AS1	ENST00000831071.1	n.-15A>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114078 AN: 151966 Hom.: 44548 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.931

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.750 AC: 114111 AN: 152082 Hom.: 44554 Cov.: 32 AF XY: 0.756 AC XY: 56222 AN XY: 74340

African (AFR) AF: 0.507 AC: 21038 AN: 41462

American (AMR) AF: 0.832 AC: 12715 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3141 AN: 3468

East Asian (EAS) AF: 0.955 AC: 4938 AN: 5168

South Asian (SAS) AF: 0.930 AC: 4485 AN: 4820

European-Finnish (FIN) AF: 0.832 AC: 8801 AN: 10580

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56243 AN: 67982

Other (OTH) AF: 0.792 AC: 1675 AN: 2114

Alfa AF: 0.763 Hom.: 6075

Bravo AF: 0.740

Asia WGS AF: 0.906 AC: 3150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	16
DANN	Benign	0.75
PhyloP100		0.53
Mutation Taster		=99/1	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: rs2388486; hg19: chr10-8099021;