rs1390950

Variant names:

• chr8-11738320-C-T
• rs1390950
• NM_001308093.3:c.617-10596C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001308093.3(GATA4):​c.617-10596C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 151,996 control chromosomes in the GnomAD database, including 40,472 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 0.72 (40472 hom., cov: 30)
• Consequence: GATA4 NM_001308093.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210

Genes affected

GATA4 (HGNC:4173): (GATA binding protein 4) This gene encodes a member of the GATA family of zinc-finger transcription factors. Members of this family recognize the GATA motif which is present in the promoters of many genes. This protein is thought to regulate genes involved in embryogenesis and in myocardial differentiation and function, and is necessary for normal testicular development. Mutations in this gene have been associated with cardiac septal defects. Additionally, alterations in gene expression have been associated with several cancer types. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATA4	NM_001308093.3	c.617-10596C>T		intron_variant	Intron 2 of 6	ENST00000532059.6	NP_001295022.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATA4	ENST00000532059.6	c.617-10596C>T		intron_variant	Intron 2 of 6	1	NM_001308093.3	ENSP00000435712.1

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109390 AN: 151878 Hom.: 40420 Cov.: 30

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.720 AC: 109500 AN: 151996 Hom.: 40472 Cov.: 30 AF XY: 0.719 AC XY: 53393 AN XY: 74268

Gnomad4 AFR AF: 0.895

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.728

Alfa AF: 0.662 Hom.: 16451

Bravo AF: 0.730

Asia WGS AF: 0.761 AC: 2645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.37

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

LitVar

Other links and lift over

dbSNP: rs1390950; hg19: chr8-11595829;