rs556967140

Variant names:

• chr8-11708535-G-A
• rs556967140
• NM_001308093.3:c.223G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-11708535-G-A
• chr8-11708535-G-C
• chr8-11708535-G-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001308093.3(GATA4):​c.223G>A​(p.Ala75Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A75S) has been classified as Benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GATA4 NM_001308093.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.809
• Publications: 0 publications found

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]

GATA4 Gene-Disease associations (from GenCC):

• atrial septal defect 2

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• structural congenital heart disease, multiple types - GATA4

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• testicular anomalies with or without congenital heart disease

  Inheritance: AD Classification: DEFINITIVE Submitted by: Ambry Genetics
• metabolic syndrome

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
• neonatal diabetes mellitus

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
• pancreatic hypoplasia-diabetes-congenital heart disease syndrome

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
• permanent neonatal diabetes mellitus

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
• transient neonatal diabetes mellitus

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
• 46,XY partial gonadal dysgenesis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• familial atrial fibrillation

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• tetralogy of fallot

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• dilated cardiomyopathy

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.18275514).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001308093.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATA4	NM_001308093.3	MANE Select	c.223G>A	p.Ala75Thr	missense	Exon 2 of 7	NP_001295022.1
	GATA4	NM_002052.5		c.223G>A	p.Ala75Thr	missense	Exon 2 of 7	NP_002043.2
	GATA4	NM_001308094.2		c.-6+7757G>A		intron	N/A	NP_001295023.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GATA4	ENST00000532059.6	TSL:1 MANE Select	c.223G>A	p.Ala75Thr	missense	Exon 2 of 7	ENSP00000435712.1
	GATA4	ENST00000335135.8	TSL:5	c.223G>A	p.Ala75Thr	missense	Exon 2 of 7	ENSP00000334458.4
	GATA4	ENST00000622443.3	TSL:5	c.223G>A	p.Ala75Thr	missense	Exon 3 of 8	ENSP00000482268.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1287380 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 632646

African (AFR) AF: 0.00 AC: 0 AN: 25580

American (AMR) AF: 0.00 AC: 0 AN: 21264

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20684

East Asian (EAS) AF: 0.00 AC: 0 AN: 29102

South Asian (SAS) AF: 0.00 AC: 0 AN: 65250

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32424

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3742

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1036106

Other (OTH) AF: 0.00 AC: 0 AN: 53228

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.082
BayesDel_addAF	Uncertain	0.064	T
BayesDel_noAF	Benign	-0.15
CADD	Benign	13
DANN	Benign	0.94
DEOGEN2	Uncertain	0.67	D
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.59	D
M_CAP	Pathogenic	0.64	D
MetaRNN	Benign	0.18	T
MetaSVM	Uncertain	0.20	D
MutationAssessor	Benign	1.2	L
PhyloP100		0.81
PrimateAI	Pathogenic	0.82	D
PROVEAN	Benign	-0.27	N
REVEL	Uncertain	0.40
Sift	Benign	0.088	T
Sift4G	Benign	0.26	T
Polyphen		0.0010	B
Vest4		0.12
MutPred		0.28		Gain of glycosylation at A75 (P = 0.0031)
MVP		0.81
MPC		0.013
ClinPred		0.068	T
GERP RS		0.010
Varity_R		0.051
gMVP		0.45
Mutation Taster		=97/3	polymorphism

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: rs556967140; hg19: chr8-11566044;