Genetic Variant NM_017719.5:c.56A>G (chr3-43303259-A-G) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_017719.5(SNRK):c.56A>G(p.Asp19Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

SNRK
NM_017719.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.32

Publications

0 publications found

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 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017719.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SNRK	NM_017719.5	MANE Select	c.56A>G	p.Asp19Gly	missense	Exon 3 of 7	NP_060189.3
SNRK	NM_001100594.2		c.56A>G	p.Asp19Gly	missense	Exon 2 of 6	NP_001094064.1	Q9NRH2-1
SNRK	NM_001330750.2		c.-30+16584A>G		intron	N/A	NP_001317679.1	E7EUC4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SNRK	ENST00000296088.12	TSL:1 MANE Select	c.56A>G	p.Asp19Gly	missense	Exon 3 of 7	ENSP00000296088.7	Q9NRH2-1
SNRK	ENST00000429705.6	TSL:1	c.56A>G	p.Asp19Gly	missense	Exon 2 of 6	ENSP00000411375.2	Q9NRH2-1
SNRK	ENST00000454177.5	TSL:2	c.56A>G	p.Asp19Gly	missense	Exon 4 of 8	ENSP00000401246.1	Q9NRH2-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions as Germline

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.69

BayesDel_addAF

Pathogenic

0.24

BayesDel_noAF

Uncertain

0.10

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.18

Eigen

Benign

-0.13

Eigen_PC

Benign

0.16

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Pathogenic

0.97

M_CAP

Benign

0.069

MetaRNN

Uncertain

0.51

MetaSVM

Benign

-0.64

MutationAssessor

Benign

-1.5

PhyloP100

9.3

PrimateAI

Pathogenic

0.92

PROVEAN

Uncertain

-2.5

REVEL

Uncertain

0.51

Sift

Benign

0.045

Sift4G

Benign

0.074

Polyphen

0.048

Vest4

0.62

MutPred

0.58

Gain of MoRF binding (P = 0.0326)

MVP

0.91

MPC

1.9

ClinPred

0.96

GERP RS

5.6

Varity_R

0.47

gMVP

0.85

Mutation Taster

=26/74

disease causing

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over