NM_001308093.3(GATA4):c.1150-107A>G AND Congenital heart disease

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jan 6, 2020
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000498104.4

Allele description [Variation Report for NM_001308093.3(GATA4):c.1150-107A>G]

NM_001308093.3(GATA4):c.1150-107A>G

Gene:

GATA4:GATA binding protein 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8p23.1

Genomic location:

Preferred name:

NM_001308093.3(GATA4):c.1150-107A>G

HGVS:

NC_000008.11:g.11758186A>G
NG_008177.2:g.86268A>G
NM_001308093.3:c.1150-107A>GMANE SELECT
NM_001308094.2:c.529-107A>G
NM_001374273.1:c.529-107A>G
NM_001374274.1:c.403-107A>G
NM_002052.5:c.1147-107A>G
NC_000008.10:g.11615695A>G
NM_002052.4:c.1147-107A>G

Links:

dbSNP: rs745379

NCBI 1000 Genomes Browser:

rs745379

Molecular consequence:

NM_001308093.3:c.1150-107A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001308094.2:c.529-107A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001374273.1:c.529-107A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001374274.1:c.403-107A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_002052.5:c.1147-107A>G - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Name:: Congenital heart disease (CHD)
Identifiers:: MONDO: MONDO:0005453; MedGen: C0152021

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000590805	Central Research Laboratory, Sri Devaraj Urs Academy of Higher Education and Research	no assertion criteria provided	Pathogenic (Jan 7, 2017)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001142385	Reproductive Health Research and Development, BGI Genomics	no assertion criteria provided	Benign (Jan 6, 2020)	germline	curation

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000590805

Central Research Laboratory, Sri Devaraj Urs Academy of Higher Education and Research

no assertion criteria provided

Pathogenic
(Jan 7, 2017)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001142385

Reproductive Health Research and Development, BGI Genomics

no assertion criteria provided

Benign
(Jan 6, 2020)

germline

curation

Description

This variant, NG_008177.2:g.86268A>G, leads to the disruption of branch point site.: SCV000590805

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	curation
Indian	unknown	yes	28	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Congenital heart diseases and their association with the variant distribution features on susceptibility genes.

Su W, Zhu P, Wang R, Wu Q, Wang M, Zhang X, Mei L, Tang J, Kumar M, Wang X, Su L, Dong N.

Clin Genet. 2017 Mar;91(3):349-354. doi: 10.1111/cge.12835. Epub 2016 Sep 5. Review.

PubMed [citation]

PMID:: 27426723

Details of each submission

From Central Research Laboratory, Sri Devaraj Urs Academy of Higher Education and Research, SCV000590805.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Indian	28	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		28	not provided	not provided	not provided

From Reproductive Health Research and Development, BGI Genomics, SCV001142385.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	not provided

Description

NG_008177.2(NM_002052.4):c.1147-107A>G in the gene GATA4 has an allele frequency of 0.510 in European (non-Finnish) subpopulation in the gnomAD database. 2668 homozygous occurrences are observed in the gnomAD database. This evidence suggests the variant to be classified as benign. ACMG/AMP criteria applied: BA1; BS2.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 4, 2024

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