Variant 20-62465895-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id is 1174638.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-62465895-C-T is described in Lovd as [Benign].

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/exons	MANE	Protein	UniProt
GATA5	NM_080473.5 linkuse as main transcript	c.852G>A	p.Lys284Lys	synonymous_variant	5/7	ENST00000252997.3	NP_536721.1	Q9BWX5
GATA5	XM_006723699.3 linkuse as main transcript	c.852G>A	p.Lys284Lys	synonymous_variant	5/7		XP_006723762.1	Q9BWX5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GATA5	ENST00000252997.3 linkuse as main transcript	c.852G>A	p.Lys284Lys	synonymous_variant	5/7	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

GnomAD3 exomes

AF:

0.474

AC:

103051

AN:

217526

Hom.:

24674

AF XY:

0.469

AC XY:

54954

AN XY:

117282

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 SAS exome

AF:

0.432

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

Gnomad4 AFR exome

AF:

0.674

Gnomad4 AMR exome

AF:

0.461

Gnomad4 ASJ exome

AF:

0.414

Gnomad4 EAS exome

AF:

0.508

Gnomad4 SAS exome

AF:

0.432

Gnomad4 FIN exome

AF:

0.471

Gnomad4 NFE exome

AF:

0.485

Gnomad4 OTH exome

AF:

0.486

GnomAD4 genome

AF:

0.533

AC:

81162

AN:

152148

Hom.:

22401

Cov.:

AF XY:

0.530

AC XY:

39453

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.673

Gnomad4 AMR

AF:

0.505

Gnomad4 ASJ

AF:

0.413

Gnomad4 EAS

AF:

0.463

Gnomad4 SAS

AF:

0.445

Gnomad4 FIN

AF:

0.449

Gnomad4 NFE

AF:

0.486

Gnomad4 OTH

AF:

0.531

Alfa

AF:

0.487

Hom.:

22838

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

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 04, 2018	- -

not specified

Benign:2

Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -

Congenital heart defects, multiple types, 5

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

7.8

DANN

Benign

0.53

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

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