Variant chr3-43303615-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 4.80

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 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_multiple_submitters_no_conflicts, 2 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	Protein	UniProt
SNRK	NM_017719.5 linkuse as main transcript	c.412A>C	p.Arg138=	synonymous_variant	3/7	ENST00000296088.12	NP_060189.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNRK	ENST00000296088.12 linkuse as main transcript	c.412A>C	p.Arg138=	synonymous_variant	3/7	1	NM_017719.5	ENSP00000296088	P1	Q9NRH2-1

Frequencies

GnomAD3 genomes

AF:

0.0285

AC:

4335

AN:

152172

Hom.:

203

Cov.:

show subpopulations

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.:

AF XY:

0.00590

AC XY:

798

AN XY:

135244

show subpopulations

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.:

AF XY:

0.00311

AC XY:

2260

AN XY:

727212

show subpopulations

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.:

AF XY:

0.0276

AC XY:

2054

AN XY:

74478

show subpopulations

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.:

Bravo

AF:

0.0319

Asia WGS

AF:

0.00635

AC:

AN:

3478

EpiCase

AF:

0.00224

EpiControl

AF:

0.00119

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over