NM_017719.5:c.1139C>G

Variant names:

• chr3-43347398-C-G
• NM_017719.5:c.1139C>G

Variant summary

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

The NM_017719.5(SNRK):​c.1139C>G​(p.Thr380Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: SNRK NM_017719.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.50

Genes affected

SNRK (HGNC:30598): (SNF related kinase) SNRK is a member of the sucrose nonfermenting (SNF)-related kinase family of serine/threonine kinases (Kertesz et al., 2002 [PubMed 12234663]).[supplied by OMIM, Apr 2009]

SNRK-AS1 (HGNC:41269): (SNRK antisense RNA 1)

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=0.06918764).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNRK	NM_017719.5	c.1139C>G	p.Thr380Ser	missense_variant	Exon 7 of 7	ENST00000296088.12	NP_060189.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNRK	ENST00000296088.12	c.1139C>G	p.Thr380Ser	missense_variant	Exon 7 of 7	1	NM_017719.5	ENSP00000296088.7

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jul 16, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1139C>G (p.T380S) alteration is located in exon 7 (coding exon 5) of the SNRK gene. This alteration results from a C to G substitution at nucleotide position 1139, causing the threonine (T) at amino acid position 380 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	0.068
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	19
DANN	Benign	0.92
DEOGEN2	Benign	0.034	T;T;T;.
Eigen	Benign	-0.32
Eigen_PC	Benign	-0.051
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Benign	0.73	.;.;T;T
M_CAP	Benign	0.0073	T
MetaRNN	Benign	0.069	T;T;T;T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	-0.97	N;N;N;.
PrimateAI	Benign	0.43	T
PROVEAN	Benign	-0.18	N;N;N;N
REVEL	Benign	0.15
Sift	Benign	0.58	T;T;T;T
Sift4G	Benign	0.72	T;T;T;T
Polyphen		0.0	B;B;B;.
Vest4		0.036
MutPred		0.17		Loss of stability (P = 0.1254);Loss of stability (P = 0.1254);Loss of stability (P = 0.1254);.;
MVP		0.30
MPC		0.50
ClinPred		0.83	D
GERP RS		5.1
Varity_R		0.15
gMVP		0.17

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: chr3-43388890;