1-24902276-G-C

Variant names:

• chr1-24902276-G-C
• rs760630862
• NM_004350.3:c.1094C>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_004350.3(RUNX3):​c.1094C>G​(p.Thr365Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: RUNX3 NM_004350.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.35

Genes affected

RUNX3 (HGNC:10473): (RUNX family transcription factor 3) This gene encodes a member of the runt domain-containing family of transcription factors. A heterodimer of this protein and a beta subunit forms a complex that binds to the core DNA sequence 5'-PYGPYGGT-3' found in a number of enhancers and promoters, and can either activate or suppress transcription. It also interacts with other transcription factors. It functions as a tumor suppressor, and the gene is frequently deleted or transcriptionally silenced in cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2235058).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RUNX3	NM_004350.3	c.1094C>G	p.Thr365Ser	missense_variant	Exon 5 of 5	ENST00000308873.11	NP_004341.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RUNX3	ENST00000308873.11	c.1094C>G	p.Thr365Ser	missense_variant	Exon 5 of 5	1	NM_004350.3	ENSP00000308051.6
RUNX3	ENST00000338888.4	c.1136C>G	p.Thr379Ser	missense_variant	Exon 7 of 7	1		ENSP00000343477.3
RUNX3	ENST00000399916.5	c.1136C>G	p.Thr379Ser	missense_variant	Exon 6 of 6	2		ENSP00000382800.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Bravo AF: 0.0000151

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Dec 14, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1136C>G (p.T379S) alteration is located in exon 6 (coding exon 6) of the RUNX3 gene. This alteration results from a C to G substitution at nucleotide position 1136, causing the threonine (T) at amino acid position 379 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.067
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.44
CADD	Benign	23
DANN	Uncertain	0.98
DEOGEN2	Uncertain	0.46	.;T;.
Eigen	Benign	0.023
Eigen_PC	Benign	0.14
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.44	T;T;.
M_CAP	Benign	0.018	T
MetaRNN	Benign	0.22	T;T;T
MetaSVM	Benign	-0.84	T
MutationAssessor	Benign	1.9	.;L;.
PrimateAI	Uncertain	0.60	T
PROVEAN	Uncertain	-2.4	N;N;N
REVEL	Benign	0.063
Sift	Benign	0.077	T;T;T
Sift4G	Benign	0.41	T;T;T
Polyphen		0.30	.;B;.
Vest4		0.093
MutPred		0.34		.;Gain of phosphorylation at T365 (P = 0.0792);.;
MVP		0.43
MPC		0.67
ClinPred		0.82	D
GERP RS		4.2
Varity_R		0.19
gMVP		0.11

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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

Other links and lift over

dbSNP: rs760630862; hg19: chr1-25228767;