NM_017719.5:c.1488C>T

Variant names:

• chr3-43347747-C-T
• rs2036617
• NM_017719.5:c.1488C>T

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.1488C>T​(p.Asp496Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0051 in 1,614,040 control chromosomes in the GnomAD database, including 325 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.025 (165 hom., cov: 32)
  • Exomes 𝑓: 0.0030 (160 hom.)
• Consequence: SNRK NM_017719.5 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.529
• Publications: 2 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=-0.54).
• BP6: Variant 3-43347747-C-T is Benign according to our data. Variant chr3-43347747-C-T is described in ClinVar as Benign. ClinVar VariationId is 791920.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.529 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0824 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.1488C>T	p.Asp496Asp	synonymous	Exon 7 of 7	NP_060189.3
	SNRK	NM_001100594.2		c.1488C>T	p.Asp496Asp	synonymous	Exon 6 of 6	NP_001094064.1	Q9NRH2-1
	SNRK	NM_001330750.2		c.870C>T	p.Asp290Asp	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.1488C>T	p.Asp496Asp	synonymous	Exon 7 of 7	ENSP00000296088.7	Q9NRH2-1
	SNRK	ENST00000429705.6	TSL:1	c.1488C>T	p.Asp496Asp	synonymous	Exon 6 of 6	ENSP00000411375.2	Q9NRH2-1
	SNRK	ENST00000454177.5	TSL:2	c.1488C>T	p.Asp496Asp	synonymous	Exon 8 of 8	ENSP00000401246.1	Q9NRH2-1

Frequencies

GnomAD3 genomes AF: 0.0250 AC: 3807 AN: 152054 Hom.: 164 Cov.: 32

Gnomad AFR AF: 0.0848

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0118

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000559

Gnomad OTH AF: 0.0187

GnomAD2 exomes AF: 0.00705 AC: 1758 AN: 249530 AF XY: 0.00561

Gnomad AFR exome AF: 0.0871

Gnomad AMR exome AF: 0.00513

Gnomad ASJ exome AF: 0.0118

Gnomad EAS exome AF: 0.000111

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000609

Gnomad OTH exome AF: 0.00594

GnomAD4 exome AF: 0.00302 AC: 4408 AN: 1461868 Hom.: 160 Cov.: 31 AF XY: 0.00269 AC XY: 1956 AN XY: 727234

African (AFR) AF: 0.0888 AC: 2973 AN: 33480

American (AMR) AF: 0.00599 AC: 268 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.0113 AC: 295 AN: 26136

East Asian (EAS) AF: 0.000101 AC: 4 AN: 39700

South Asian (SAS) AF: 0.000116 AC: 10 AN: 86258

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53394

Middle Eastern (MID) AF: 0.00451 AC: 26 AN: 5768

European-Non Finnish (NFE) AF: 0.000374 AC: 416 AN: 1112012

Other (OTH) AF: 0.00689 AC: 416 AN: 60396

GnomAD4 genome AF: 0.0251 AC: 3819 AN: 152172 Hom.: 165 Cov.: 32 AF XY: 0.0240 AC XY: 1788 AN XY: 74402

African (AFR) AF: 0.0847 AC: 3515 AN: 41478

American (AMR) AF: 0.0118 AC: 181 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3472

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5160

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10602

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

European-Non Finnish (NFE) AF: 0.000559 AC: 38 AN: 68020

Other (OTH) AF: 0.0209 AC: 44 AN: 2110

Alfa AF: 0.0123 Hom.: 59

Bravo AF: 0.0294

Asia WGS AF: 0.00982 AC: 34 AN: 3478

EpiCase AF: 0.000981

EpiControl AF: 0.000948

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	-0.54
CADD	Benign	2.5
DANN	Benign	0.84
PhyloP100		-0.53
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: rs2036617; hg19: chr3-43389239; COSMIC: COSV56066053; COSMIC: COSV56066053;