Variant 18-22172111-TACCACCACCACCACC-TACCACCACCACCACCACC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2

The NM_005257.6(GATA6):c.996_998dup(p.His332dup) variant causes a inframe insertion change. The variant allele was found at a frequency of 0.00123 in 1,463,724 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0015 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0012 ( 1 hom. )

Consequence

GATA6
NM_005257.6 inframe_insertion

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 4.59

Variant links:

Genes affected

GATA6 (HGNC:4174): (GATA binding protein 6) This gene is a member of a small family of zinc finger transcription factors that play an important role in the regulation of cellular differentiation and organogenesis during vertebrate development. This gene is expressed during early embryogenesis and localizes to endo- and mesodermally derived cells during later embryogenesis and thereby plays an important role in gut, lung, and heart development. Mutations in this gene are associated with several congenital defects. [provided by RefSeq, Mar 2012]

GATA6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP6

Variant 18-22172111-T-TACC is Benign according to our data. Variant chr18-22172111-T-TACC is described in ClinVar as [Likely_benign]. Clinvar id is 404060.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 227 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GATA6	NM_005257.6 linkuse as main transcript	c.996_998dup	p.His332dup	inframe_insertion	2/7	ENST00000269216.10	NP_005248.2
GATA6	XM_047437483.1 linkuse as main transcript	c.996_998dup	p.His332dup	inframe_insertion	2/7		XP_047293439.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GATA6	ENST00000269216.10 linkuse as main transcript	c.996_998dup	p.His332dup	inframe_insertion	2/7	1	NM_005257.6	ENSP00000269216	P1	Q92908-1
GATA6	ENST00000581694.1 linkuse as main transcript	c.996_998dup	p.His332dup	inframe_insertion	1/6	1		ENSP00000462313	P1	Q92908-1

Frequencies

GnomAD3 genomes

AF:

0.00153

AC:

229

AN:

149900

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00249

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000924

Gnomad ASJ

AF:

0.00116

Gnomad EAS

AF:

0.000995

Gnomad SAS

AF:

0.00147

Gnomad FIN

AF:

0.000196

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00142

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00150

AC:

AN:

48518

Hom.:

AF XY:

0.00142

AC XY:

AN XY:

26132

show subpopulations

Gnomad AFR exome

AF:

0.00560

Gnomad AMR exome

AF:

0.00153

Gnomad ASJ exome

AF:

0.00106

Gnomad EAS exome

AF:

0.000466

Gnomad SAS exome

AF:

0.00196

Gnomad FIN exome

AF:

0.00110

Gnomad NFE exome

AF:

0.00124

Gnomad OTH exome

AF:

0.000657

GnomAD4 exome

AF:

0.00119

AC:

1568

AN:

1313728

Hom.:

Cov.:

AF XY:

0.00114

AC XY:

733

AN XY:

644874

show subpopulations

Gnomad4 AFR exome

AF:

0.00254

Gnomad4 AMR exome

AF:

0.000742

Gnomad4 ASJ exome

AF:

0.000787

Gnomad4 EAS exome

AF:

0.000619

Gnomad4 SAS exome

AF:

0.00118

Gnomad4 FIN exome

AF:

0.000886

Gnomad4 NFE exome

AF:

0.00122

Gnomad4 OTH exome

AF:

0.00105

GnomAD4 genome

AF:

0.00151

AC:

227

AN:

149996

Hom.:

Cov.:

AF XY:

0.00132

AC XY:

AN XY:

73208

show subpopulations

Gnomad4 AFR

AF:

0.00246

Gnomad4 AMR

AF:

0.000857

Gnomad4 ASJ

AF:

0.00116

Gnomad4 EAS

AF:

0.000998

Gnomad4 SAS

AF:

0.00147

Gnomad4 FIN

AF:

0.000196

Gnomad4 NFE

AF:

0.00142

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

May 24, 2021

- -

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 08, 2022

See Variant Classification Assertion Criteria. -

GATA6-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 28, 2020

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Atrioventricular septal defect 5

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 22, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over