chr20-62465397-C-G

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_080473.5(GATA5):c.981G>C(p.Ser327Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 1,604,128 control chromosomes in the GnomAD database, including 198,932 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.54 ( 22497 hom., cov: 33)

Exomes 𝑓: 0.49 ( 176435 hom. )

Consequence

GATA5
NM_080473.5 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.05

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 20-62465397-C-G is Benign according to our data. Variant chr20-62465397-C-G is described in ClinVar as [Benign]. Clinvar id is 1174882.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-62465397-C-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=1.05 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GATA5	NM_080473.5 link	c.981G>C	p.Ser327Ser	synonymous_variant	Exon 6 of 7	ENST00000252997.3	NP_536721.1	Q9BWX5
GATA5	XM_006723699.3 link	c.981G>C	p.Ser327Ser	synonymous_variant	Exon 6 of 7		XP_006723762.1	Q9BWX5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATA5	ENST00000252997.3 link	c.981G>C	p.Ser327Ser	synonymous_variant	Exon 6 of 7	1	NM_080473.5	ENSP00000252997.2		Q9BWX5

Frequencies

GnomAD3 genomes

AF:

0.536

AC:

81325

AN:

151754

Hom.:

22458

Cov.:

show subpopulations

Gnomad AFR

AF:

0.669

Gnomad AMI

AF:

0.496

Gnomad AMR

AF:

0.505

Gnomad ASJ

AF:

0.416

Gnomad EAS

AF:

0.493

Gnomad SAS

AF:

0.448

Gnomad FIN

AF:

0.453

Gnomad MID

AF:

0.478

Gnomad NFE

AF:

0.491

Gnomad OTH

AF:

0.530

GnomAD3 exomes

AF:

0.486

AC:

118556

AN:

243820

Hom.:

29339

AF XY:

0.481

AC XY:

63824

AN XY:

132648

show subpopulations

Gnomad AFR exome

AF:

0.667

Gnomad AMR exome

AF:

0.460

Gnomad ASJ exome

AF:

0.420

Gnomad EAS exome

AF:

0.481

Gnomad SAS exome

AF:

0.436

Gnomad FIN exome

AF:

0.466

Gnomad NFE exome

AF:

0.492

Gnomad OTH exome

AF:

0.485

GnomAD4 exome

AF:

0.491

AC:

713576

AN:

1452256

Hom.:

176435

Cov.:

AF XY:

0.489

AC XY:

353288

AN XY:

722564

show subpopulations

Gnomad4 AFR exome

AF:

0.671

Gnomad4 AMR exome

AF:

0.465

Gnomad4 ASJ exome

AF:

0.420

Gnomad4 EAS exome

AF:

0.536

Gnomad4 SAS exome

AF:

0.434

Gnomad4 FIN exome

AF:

0.482

Gnomad4 NFE exome

AF:

0.492

Gnomad4 OTH exome

AF:

0.494

GnomAD4 genome

AF:

0.536

AC:

81421

AN:

151872

Hom.:

22497

Cov.:

AF XY:

0.533

AC XY:

39599

AN XY:

74238

show subpopulations

Gnomad4 AFR

AF:

0.669

Gnomad4 AMR

AF:

0.506

Gnomad4 ASJ

AF:

0.416

Gnomad4 EAS

AF:

0.492

Gnomad4 SAS

AF:

0.448

Gnomad4 FIN

AF:

0.453

Gnomad4 NFE

AF:

0.491

Gnomad4 OTH

AF:

0.532

Alfa

AF:

0.417

Hom.:

1973

Bravo

AF:

0.543

Asia WGS

AF:

0.502

AC:

1749

AN:

3478

EpiCase

AF:

0.486

EpiControl

AF:

0.486

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Sep 06, 2018

GeneDx

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

-0.77

CADD

Benign

6.8

DANN

Benign

0.52

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