chr3-43303248-A-G

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_017719.5(SNRK):ā€‹c.45A>Gā€‹(p.Leu15=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00444 in 1,614,148 control chromosomes in the GnomAD database, including 298 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā˜…ā˜…).

Frequency

Genomes: š‘“ 0.024 ( 148 hom., cov: 32)
Exomes š‘“: 0.0025 ( 150 hom. )

Consequence

SNRK
NM_017719.5 synonymous

Scores

2

Clinical Significance

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

Conservation

PhyloP100: 0.670
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
Variant 3-43303248-A-G is Benign according to our data. Variant chr3-43303248-A-G is described in ClinVar as [Benign]. Clinvar id is 791918.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.67 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0786 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SNRKNM_017719.5 linkuse as main transcriptc.45A>G p.Leu15= synonymous_variant 3/7 ENST00000296088.12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SNRKENST00000296088.12 linkuse as main transcriptc.45A>G p.Leu15= synonymous_variant 3/71 NM_017719.5 P1Q9NRH2-1

Frequencies

GnomAD3 genomes
AF:
0.0235
AC:
3575
AN:
152176
Hom.:
147
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0810
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0111
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00633
Gnomad NFE
AF:
0.000250
Gnomad OTH
AF:
0.0154
GnomAD3 exomes
AF:
0.00603
AC:
1503
AN:
249274
Hom.:
71
AF XY:
0.00461
AC XY:
623
AN XY:
135250
show subpopulations
Gnomad AFR exome
AF:
0.0834
Gnomad AMR exome
AF:
0.00455
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000981
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000239
Gnomad OTH exome
AF:
0.00413
GnomAD4 exome
AF:
0.00246
AC:
3592
AN:
1461854
Hom.:
150
Cov.:
31
AF XY:
0.00211
AC XY:
1532
AN XY:
727220
show subpopulations
Gnomad4 AFR exome
AF:
0.0854
Gnomad4 AMR exome
AF:
0.00548
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000696
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000133
Gnomad4 OTH exome
AF:
0.00525
GnomAD4 genome
AF:
0.0235
AC:
3582
AN:
152294
Hom.:
148
Cov.:
32
AF XY:
0.0227
AC XY:
1691
AN XY:
74480
show subpopulations
Gnomad4 AFR
AF:
0.0809
Gnomad4 AMR
AF:
0.0110
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000250
Gnomad4 OTH
AF:
0.0152
Alfa
AF:
0.0105
Hom.:
42
Bravo
AF:
0.0278
Asia WGS
AF:
0.00346
AC:
12
AN:
3478
EpiCase
AF:
0.000218
EpiControl
AF:
0.000296

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 submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.54
CADD
Benign
5.8
DANN
Benign
0.72

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.

Other links and lift over

dbSNP: rs17075519; hg19: chr3-43344740; API