10-8055665-A-T

Variant names:

• chr10-8055665-A-T
• NM_001002295.2:c.10A>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001002295.2(GATA3):​c.10A>T​(p.Thr4Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000712 in 1,404,162 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: GATA3 NM_001002295.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.11086717).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATA3	NM_001002295.2	c.10A>T	p.Thr4Ser	missense_variant	Exon 2 of 6	ENST00000379328.9	NP_001002295.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATA3	ENST00000379328.9	c.10A>T	p.Thr4Ser	missense_variant	Exon 2 of 6	1	NM_001002295.2	ENSP00000368632.3
GATA3	ENST00000346208.4	c.10A>T	p.Thr4Ser	missense_variant	Exon 2 of 6	1		ENSP00000341619.3
GATA3	ENST00000481743.2	c.10A>T	p.Thr4Ser	missense_variant	Exon 2 of 3	2		ENSP00000493486.1
GATA3	ENST00000643001.1	c.10A>T	p.Thr4Ser	missense_variant	Exon 2 of 2			ENSP00000494284.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.12e-7 AC: 1 AN: 1404162 Hom.: 0 Cov.: 33 AF XY: 0.00000144 AC XY: 1 AN XY: 693370

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.24e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.065
BayesDel_addAF	Benign	-0.018	T
BayesDel_noAF	Benign	-0.26
CADD	Benign	20
DANN	Benign	0.93
DEOGEN2	Benign	0.34	.;.;.;.;T
Eigen	Benign	-0.45
Eigen_PC	Benign	-0.21
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Benign	0.77	T;T;.;T;T
M_CAP	Uncertain	0.28	D
MetaRNN	Benign	0.11	T;T;T;T;T
MetaSVM	Benign	-0.40	T
MutationAssessor	Benign	-0.81	.;.;N;N;N
PrimateAI	Uncertain	0.65	T
PROVEAN	Benign	0.34	.;.;N;.;N
REVEL	Benign	0.27
Sift	Benign	0.92	.;.;T;.;T
Sift4G	Benign	1.0	.;.;T;.;T
Polyphen		0.0	.;.;B;B;B
Vest4		0.037, 0.035
MutPred		0.14		Gain of disorder (P = 0.0694);Gain of disorder (P = 0.0694);Gain of disorder (P = 0.0694);Gain of disorder (P = 0.0694);Gain of disorder (P = 0.0694);
MVP		0.44
MPC		0.66
ClinPred		0.29	T
GERP RS		4.6
Varity_R		0.058
gMVP		0.18

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-8097628;