5-173233001-C-T

Position:

chr5-173233001-C-T

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2

The NM_004387.4(NKX2-5):c.543G>A(p.Gln181Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00643 in 1,611,374 control chromosomes in the GnomAD database, including 69 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0060 ( 8 hom., cov: 32)

Exomes 𝑓: 0.0065 ( 61 hom. )

Consequence

NKX2-5
NM_004387.4 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:16

Conservation

PhyloP100: 3.37

Variant links:

Genes affected

NKX2-5 (HGNC:2488): (NK2 homeobox 5) This gene encodes a homeobox-containing transcription factor. This transcription factor functions in heart formation and development. Mutations in this gene cause atrial septal defect with atrioventricular conduction defect, and also tetralogy of Fallot, which are both heart malformation diseases. Mutations in this gene can also cause congenital hypothyroidism non-goitrous type 5, a non-autoimmune condition. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

NKX2-5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP6

Variant 5-173233001-C-T is Benign according to our data. Variant chr5-173233001-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 36658.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-173233001-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=3.37 with no splicing effect.

BS1

Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00601 (916/152350) while in subpopulation AMR AF= 0.0113 (173/15308). AF 95% confidence interval is 0.00993. There are 8 homozygotes in gnomad4. There are 435 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 8 SD gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NKX2-5	NM_004387.4 linkuse as main transcript	c.543G>A	p.Gln181Gln	synonymous_variant	2/2	ENST00000329198.5	NP_004378.1	P52952-1A0A0S2Z383
NKX2-5	NM_001166176.2 linkuse as main transcript	c.*342G>A		3_prime_UTR_variant	2/2		NP_001159648.1	P52952-2
NKX2-5	NM_001166175.2 linkuse as main transcript	c.*496G>A		3_prime_UTR_variant	2/2		NP_001159647.1	P52952-3A0A0S2Z3K2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
NKX2-5	ENST00000329198.5 linkuse as main transcript	c.543G>A	p.Gln181Gln	synonymous_variant	2/2	1	NM_004387.4	ENSP00000327758.4	P52952-1
NKX2-5	ENST00000424406 linkuse as main transcript	c.*496G>A		3_prime_UTR_variant	2/2	1		ENSP00000395378.2	P52952-3
NKX2-5	ENST00000521848 linkuse as main transcript	c.*342G>A		3_prime_UTR_variant	2/2	2		ENSP00000427906.1	P52952-2

Frequencies

GnomAD3 genomes

AF:

0.00603

AC:

918

AN:

152232

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00111

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0113

Gnomad ASJ

AF:

0.0349

Gnomad EAS

AF:

0.000963

Gnomad SAS

AF:

0.00932

Gnomad FIN

AF:

0.00216

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.00689

Gnomad OTH

AF:

0.0110

GnomAD3 exomes

AF:

0.00748

AC:

1836

AN:

245362

Hom.:

AF XY:

0.00798

AC XY:

1063

AN XY:

133228

show subpopulations

Gnomad AFR exome

AF:

0.000770

Gnomad AMR exome

AF:

0.00742

Gnomad ASJ exome

AF:

0.0338

Gnomad EAS exome

AF:

0.0000553

Gnomad SAS exome

AF:

0.0117

Gnomad FIN exome

AF:

0.00292

Gnomad NFE exome

AF:

0.00693

Gnomad OTH exome

AF:

0.00913

GnomAD4 exome

AF:

0.00647

AC:

9447

AN:

1459024

Hom.:

Cov.:

AF XY:

0.00685

AC XY:

4968

AN XY:

725720

show subpopulations

Gnomad4 AFR exome

AF:

0.00129

Gnomad4 AMR exome

AF:

0.00833

Gnomad4 ASJ exome

AF:

0.0340

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0125

Gnomad4 FIN exome

AF:

0.00291

Gnomad4 NFE exome

AF:

0.00564

Gnomad4 OTH exome

AF:

0.00888

GnomAD4 genome

AF:

0.00601

AC:

916

AN:

152350

Hom.:

Cov.:

AF XY:

0.00584

AC XY:

435

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.00108

Gnomad4 AMR

AF:

0.0113

Gnomad4 ASJ

AF:

0.0349

Gnomad4 EAS

AF:

0.000965

Gnomad4 SAS

AF:

0.00912

Gnomad4 FIN

AF:

0.00216

Gnomad4 NFE

AF:

0.00689

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.00726

Hom.:

Bravo

AF:

0.00628

Asia WGS

AF:

0.00462

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:16

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:8

Benign, criteria provided, single submitter	clinical testing	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia	Jul 10, 2015	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Dec 02, 2013	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Feb 08, 2013	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 29, 2016	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency in ESP (all): 70/13004=0.53% -

not provided

Benign:4

Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 11, 2018	This variant is associated with the following publications: (PMID: 22995991, 20981092, 19464101, 24376681, 27884173, 27535533) -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Dec 01, 2022	- -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2024	NKX2-5: BP4, BS1, BS2 -

Atrial septal defect 7

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Atrial septal defect

Benign:1

Benign, no assertion criteria provided

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Jan 07, 2015

- -

Lissencephaly due to TUBA1A mutation

Benign:1

Benign, criteria provided, single submitter

research

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

The heterozygous c.543G>A (p.Gln181=) variant in NKX2-5 has been identified in at least 2 individuals with cardiac disease (PMID: 19464101, 24376681) but has also been identified in >1% of South Asian chromosomes and 7 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In summary, this variant meets criteria to be classified as benign for cardiac disease. -

Cardiovascular phenotype

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

May 04, 2015

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Benign

0.97

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