5-173235011-G-C

Variant names:

• chr5-173235011-G-C
• NM_004387.4:c.73C>G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM2 PM5 BP4_Moderate

The NM_004387.4(NKX2-5):​c.73C>G​(p.Arg25Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R25C) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: NKX2-5 NM_004387.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.972

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr5-173235011-G-A is described in Lovd as [Likely_pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.157776).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NKX2-5	NM_004387.4	c.73C>G	p.Arg25Gly	missense_variant	Exon 1 of 2	ENST00000329198.5	NP_004378.1
NKX2-5	NM_001166176.2	c.73C>G	p.Arg25Gly	missense_variant	Exon 1 of 2		NP_001159648.1
NKX2-5	NM_001166175.2	c.73C>G	p.Arg25Gly	missense_variant	Exon 1 of 2		NP_001159647.1
NKX2-5	XM_017009071.3	c.73C>G	p.Arg25Gly	missense_variant	Exon 1 of 2		XP_016864560.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NKX2-5	ENST00000329198.5	c.73C>G	p.Arg25Gly	missense_variant	Exon 1 of 2	1	NM_004387.4	ENSP00000327758.4
NKX2-5	ENST00000424406.2	c.73C>G	p.Arg25Gly	missense_variant	Exon 1 of 2	1		ENSP00000395378.2
NKX2-5	ENST00000521848.1	c.73C>G	p.Arg25Gly	missense_variant	Exon 1 of 2	2		ENSP00000427906.1
NKX2-5	ENST00000517440.1	c.73C>G	p.Arg25Gly	missense_variant	Exon 1 of 2	4		ENSP00000429905.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.081
BayesDel_addAF	Benign	-0.010	T
BayesDel_noAF	Benign	-0.25
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.41	T;.;.;T
Eigen	Benign	-0.43
Eigen_PC	Benign	-0.25
FATHMM_MKL	Uncertain	0.78	D
LIST_S2	Benign	0.23	T;T;T;T
M_CAP	Uncertain	0.21	D
MetaRNN	Benign	0.16	T;T;T;T
MetaSVM	Benign	-0.65	T
MutationAssessor	Benign	1.0	L;L;L;.
PrimateAI	Uncertain	0.68	T
PROVEAN	Benign	-0.37	N;N;N;N
REVEL	Benign	0.18
Sift	Benign	0.15	T;T;T;T
Sift4G	Benign	0.15	T;T;T;.
Polyphen		0.0	B;.;.;B
Vest4		0.099
MutPred		0.37		Gain of glycosylation at S26 (P = 0.0593);Gain of glycosylation at S26 (P = 0.0593);Gain of glycosylation at S26 (P = 0.0593);Gain of glycosylation at S26 (P = 0.0593);
MVP		0.79
MPC		1.5
ClinPred		0.50	T
GERP RS		3.9
Varity_R		0.13
gMVP		0.36

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-172662014;