3-43303615-A-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_017719.5(SNRK):c.412A>C(p.Arg138=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00582 in 1,614,132 control chromosomes in the GnomAD database, including 374 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.028 (203 hom., cov: 32)
  • Exomes 𝑓: 0.0035 (171 hom.)
• Consequence: SNRK NM_017719.5 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 4.80

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BP6: Variant 3-43303615-A-C is Benign according to our data. Variant chr3-43303615-A-C is described in ClinVar as [Benign]. Clinvar id is 775863.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNRK	NM_017719.5	c.412A>C	p.Arg138=	synonymous_variant	3/7	ENST00000296088.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNRK	ENST00000296088.12	c.412A>C	p.Arg138=	synonymous_variant	3/7	1	NM_017719.5	P1

Frequencies

GnomAD3 genomes AF: 0.0285 AC: 4335 AN: 152172 Hom.: 203 Cov.: 32

Gnomad AFR AF: 0.0973

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0118

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00110

Gnomad OTH AF: 0.0187

GnomAD3 exomes AF: 0.00774 AC: 1929 AN: 249266 Hom.: 96 AF XY: 0.00590 AC XY: 798 AN XY: 135244

Gnomad AFR exome AF: 0.102

Gnomad AMR exome AF: 0.00507

Gnomad ASJ exome AF: 0.00139

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000686

Gnomad FIN exome AF: 0.0000464

Gnomad NFE exome AF: 0.000893

Gnomad OTH exome AF: 0.00595

GnomAD4 exome AF: 0.00346 AC: 5052 AN: 1461842 Hom.: 171 Cov.: 31 AF XY: 0.00311 AC XY: 2260 AN XY: 727212

Gnomad4 AFR exome AF: 0.0997

Gnomad4 AMR exome AF: 0.00593

Gnomad4 ASJ exome AF: 0.00149

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000614

Gnomad4 FIN exome AF: 0.0000374

Gnomad4 NFE exome AF: 0.000738

Gnomad4 OTH exome AF: 0.00763

GnomAD4 genome AF: 0.0285 AC: 4340 AN: 152290 Hom.: 203 Cov.: 32 AF XY: 0.0276 AC XY: 2054 AN XY: 74478

Gnomad4 AFR AF: 0.0971

Gnomad4 AMR AF: 0.0118

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000622

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00110

Gnomad4 OTH AF: 0.0185

Alfa AF: 0.0116 Hom.: 47

Bravo AF: 0.0319

Asia WGS AF: 0.00635 AC: 23 AN: 3478

EpiCase AF: 0.00224

EpiControl AF: 0.00119

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
Cadd	Benign	11
Dann	Benign	0.63

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

LitVar

Other links and lift over

dbSNP: rs17075521; hg19: chr3-43345107;