NM_017719.5:c.1758A>G

Variant names:

• chr3-43348017-A-G
• rs34730190
• NM_017719.5:c.1758A>G

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_017719.5(SNRK):​c.1758A>G​(p.Pro586Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0054 in 1,611,912 control chromosomes in the GnomAD database, including 373 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.027 (189 hom., cov: 32)
  • Exomes 𝑓: 0.0032 (184 hom.)
• Consequence: SNRK NM_017719.5 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.45
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 3-43348017-A-G is Benign according to our data. Variant chr3-43348017-A-G is described in ClinVar as Benign. ClinVar VariationId is 791921.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-2.45 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0887 is higher than 0.05.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNRK	NM_017719.5	MANE Select	c.1758A>G	p.Pro586Pro	synonymous	Exon 7 of 7	NP_060189.3
	SNRK	NM_001100594.2		c.1758A>G	p.Pro586Pro	synonymous	Exon 6 of 6	NP_001094064.1	Q9NRH2-1
	SNRK	NM_001330750.2		c.1140A>G	p.Pro380Pro	synonymous	Exon 5 of 5	NP_001317679.1	E7EUC4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNRK	ENST00000296088.12	TSL:1 MANE Select	c.1758A>G	p.Pro586Pro	synonymous	Exon 7 of 7	ENSP00000296088.7	Q9NRH2-1
	SNRK	ENST00000429705.6	TSL:1	c.1758A>G	p.Pro586Pro	synonymous	Exon 6 of 6	ENSP00000411375.2	Q9NRH2-1
	SNRK	ENST00000454177.5	TSL:2	c.1758A>G	p.Pro586Pro	synonymous	Exon 8 of 8	ENSP00000401246.1	Q9NRH2-1

Frequencies

GnomAD3 genomes AF: 0.0269 AC: 4086 AN: 152142 Hom.: 188 Cov.: 32

Gnomad AFR AF: 0.0912

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0126

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000529

Gnomad OTH AF: 0.0191

GnomAD2 exomes AF: 0.00739 AC: 1809 AN: 244756 AF XY: 0.00587

Gnomad AFR exome AF: 0.0930

Gnomad AMR exome AF: 0.00526

Gnomad ASJ exome AF: 0.0121

Gnomad EAS exome AF: 0.000112

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000571

Gnomad OTH exome AF: 0.00590

GnomAD4 exome AF: 0.00315 AC: 4599 AN: 1459652 Hom.: 184 Cov.: 31 AF XY: 0.00279 AC XY: 2024 AN XY: 726092

African (AFR) AF: 0.0955 AC: 3194 AN: 33450

American (AMR) AF: 0.00613 AC: 273 AN: 44542

Ashkenazi Jewish (ASJ) AF: 0.0113 AC: 292 AN: 25872

East Asian (EAS) AF: 0.0000756 AC: 3 AN: 39700

South Asian (SAS) AF: 0.0000698 AC: 6 AN: 86004

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53192

Middle Eastern (MID) AF: 0.00435 AC: 25 AN: 5750

European-Non Finnish (NFE) AF: 0.000329 AC: 366 AN: 1110836

Other (OTH) AF: 0.00730 AC: 440 AN: 60306

GnomAD4 genome AF: 0.0269 AC: 4098 AN: 152260 Hom.: 189 Cov.: 32 AF XY: 0.0257 AC XY: 1912 AN XY: 74468

African (AFR) AF: 0.0911 AC: 3784 AN: 41534

American (AMR) AF: 0.0125 AC: 192 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5170

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10626

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000529 AC: 36 AN: 68006

Other (OTH) AF: 0.0213 AC: 45 AN: 2116

Alfa AF: 0.00945 Hom.: 37

Bravo AF: 0.0314

Asia WGS AF: 0.0110 AC: 37 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.46
PhyloP100		-2.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs34730190; hg19: chr3-43389509;