chr3-43348287-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_017719.5(SNRK):ā€‹c.2028T>Gā€‹(p.Ser676Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,613,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.000020 ( 0 hom., cov: 32)
Exomes š‘“: 0.0000075 ( 0 hom. )

Consequence

SNRK
NM_017719.5 missense

Scores

5
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.477
Variant links:
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)

Genome browser will be placed here

ACMG classification

Classification made for transcript

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=0.12935406).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SNRKNM_017719.5 linkuse as main transcriptc.2028T>G p.Ser676Arg missense_variant 7/7 ENST00000296088.12
SNRK-AS1NR_046757.1 linkuse as main transcriptn.2107A>C non_coding_transcript_exon_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SNRKENST00000296088.12 linkuse as main transcriptc.2028T>G p.Ser676Arg missense_variant 7/71 NM_017719.5 P1Q9NRH2-1
SNRK-AS1ENST00000607513.2 linkuse as main transcriptn.626A>C non_coding_transcript_exon_variant 3/3

Frequencies

GnomAD3 genomes
AF:
0.0000197
AC:
3
AN:
152140
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000753
AC:
11
AN:
1461752
Hom.:
0
Cov.:
31
AF XY:
0.00000688
AC XY:
5
AN XY:
727186
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000989
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000197
AC:
3
AN:
152140
Hom.:
0
Cov.:
32
AF XY:
0.0000135
AC XY:
1
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000142
Hom.:
0
Bravo
AF:
0.0000189
ExAC
AF:
0.00000828
AC:
1

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMar 20, 2023The c.2028T>G (p.S676R) alteration is located in exon 7 (coding exon 5) of the SNRK gene. This alteration results from a T to G substitution at nucleotide position 2028, causing the serine (S) at amino acid position 676 to be replaced by an arginine (R). 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
Uncertain
0.50
BayesDel_addAF
Benign
-0.031
T
BayesDel_noAF
Benign
-0.28
CADD
Benign
12
DANN
Uncertain
0.97
DEOGEN2
Benign
0.056
T;T;T;.
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.2
FATHMM_MKL
Benign
0.16
N
LIST_S2
Benign
0.79
.;.;T;T
M_CAP
Uncertain
0.21
D
MetaRNN
Benign
0.13
T;T;T;T
MetaSVM
Benign
-0.93
T
MutationAssessor
Benign
0.90
L;L;L;.
MutationTaster
Benign
0.94
D;D;D;D
PrimateAI
Uncertain
0.58
T
PROVEAN
Benign
-0.87
N;N;N;N
REVEL
Benign
0.17
Sift
Uncertain
0.0010
D;D;D;D
Sift4G
Benign
0.48
T;T;T;T
Polyphen
0.38
B;B;B;.
Vest4
0.31
MutPred
0.38
Gain of MoRF binding (P = 0.0184);Gain of MoRF binding (P = 0.0184);Gain of MoRF binding (P = 0.0184);.;
MVP
0.40
MPC
1.6
ClinPred
0.30
T
GERP RS
-6.4
Varity_R
0.48
gMVP
0.40

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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.

Other links and lift over

dbSNP: rs748632098; hg19: chr3-43389779; API