chr20-62465895-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_080473.5(GATA5):c.852G>A(p.Lys284Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 1,594,492 control chromosomes in the GnomAD database, including 193,228 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.53 ( 22401 hom., cov: 34)

Exomes 𝑓: 0.48 ( 170827 hom. )

Consequence

GATA5
NM_080473.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -0.0710

Publications

25 publications found

Variant links:

Genes affected

GATA5 (HGNC:15802): (GATA binding protein 5) The protein encoded by this gene is a transcription factor that contains two GATA-type zinc fingers. The encoded protein is known to bind to hepatocyte nuclear factor-1alpha (HNF-1alpha), and this interaction is essential for cooperative activation of the intestinal lactase-phlorizin hydrolase promoter. In other organisms, similar proteins may be involved in the establishment of cardiac smooth muscle cell diversity. [provided by RefSeq, Jul 2008]

GATA5 Gene-Disease associations (from GenCC):

familial atrial fibrillation
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
familial bicuspid aortic valve
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
tetralogy of fallot
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
congenital heart defects, multiple types, 5
Inheritance: AD, Unknown Classification: LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

GATA5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BP6

Variant 20-62465895-C-T is Benign according to our data. Variant chr20-62465895-C-T is described in ClinVar as Benign. ClinVar VariationId is 1174638.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.071 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATA5	NM_080473.5 link	c.852G>A	p.Lys284Lys	synonymous_variant	Exon 5 of 7	ENST00000252997.3	NP_536721.1	Q9BWX5
GATA5	XM_006723699.3 link	c.852G>A	p.Lys284Lys	synonymous_variant	Exon 5 of 7		XP_006723762.1	Q9BWX5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATA5	ENST00000252997.3 link	c.852G>A	p.Lys284Lys	synonymous_variant	Exon 5 of 7	1	NM_080473.5	ENSP00000252997.2		Q9BWX5

Frequencies

GnomAD3 genomes

AF:

0.533

AC:

81069

AN:

152030

Hom.:

22362

Cov.:

show subpopulations

Gnomad AFR

AF:

0.673

Gnomad AMI

AF:

0.487

Gnomad AMR

AF:

0.505

Gnomad ASJ

AF:

0.413

Gnomad EAS

AF:

0.465

Gnomad SAS

AF:

0.445

Gnomad FIN

AF:

0.449

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.486

Gnomad OTH

AF:

0.530

GnomAD2 exomes

AF:

0.474

AC:

103051

AN:

217526

AF XY:

0.469

show subpopulations

Gnomad AFR exome

AF:

0.664

Gnomad AMR exome

AF:

0.456

Gnomad ASJ exome

AF:

0.414

Gnomad EAS exome

AF:

0.444

Gnomad FIN exome

AF:

0.459

Gnomad NFE exome

AF:

0.479

Gnomad OTH exome

AF:

0.478

GnomAD4 exome

AF:

0.485

AC:

699016

AN:

1442344

Hom.:

170827

Cov.:

AF XY:

0.482

AC XY:

344976

AN XY:

715542

show subpopulations

African (AFR)

AF:

0.674

AC:

22367

AN:

33178

American (AMR)

AF:

0.461

AC:

19447

AN:

42184

Ashkenazi Jewish (ASJ)

AF:

0.414

AC:

10668

AN:

25738

East Asian (EAS)

AF:

0.508

AC:

19805

AN:

38980

South Asian (SAS)

AF:

0.432

AC:

35891

AN:

83174

European-Finnish (FIN)

AF:

0.471

AC:

24257

AN:

51524

Middle Eastern (MID)

AF:

0.431

AC:

2451

AN:

5684

European-Non Finnish (NFE)

AF:

0.485

AC:

535134

AN:

1102272

Other (OTH)

AF:

0.486

AC:

28996

AN:

59610

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.459

Heterozygous variant carriers

18710

37419

56129

74838

93548

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15814

31628

47442

63256

79070

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.533

AC:

81162

AN:

152148

Hom.:

22401

Cov.:

AF XY:

0.530

AC XY:

39453

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.673

AC:

27954

AN:

41536

American (AMR)

AF:

0.505

AC:

7735

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.413

AC:

1432

AN:

3470

East Asian (EAS)

AF:

0.463

AC:

2388

AN:

5154

South Asian (SAS)

AF:

0.445

AC:

2147

AN:

4824

European-Finnish (FIN)

AF:

0.449

AC:

4759

AN:

10588

Middle Eastern (MID)

AF:

0.493

AC:

145

AN:

294

European-Non Finnish (NFE)

AF:

0.486

AC:

33038

AN:

67956

Other (OTH)

AF:

0.531

AC:

1122

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1914

3827

5741

7654

9568

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

696

1392

2088

2784

3480

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.493

Hom.:

40289

Bravo

AF:

0.541

Asia WGS

AF:

0.490

AC:

1707

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Sep 04, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:2

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Congenital heart defects, multiple types, 5

Benign:1

Aug 10, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

7.8

(source)

DANN

Benign

0.53

PhyloP100

-0.071

Mutation Taster

=98/2

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over