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GeneBe

3-43348017-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_017719.5(SNRK):c.1758A>G(p.Pro586=) 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

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.45
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-AS1 (HGNC:41269): (SNRK antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-43348017-A-G is Benign according to our data. Variant chr3-43348017-A-G is described in ClinVar as [Benign]. Clinvar id is 791921.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-2.45 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0887 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SNRKNM_017719.5 linkuse as main transcriptc.1758A>G p.Pro586= synonymous_variant 7/7 ENST00000296088.12
SNRK-AS1NR_046757.1 linkuse as main transcriptn.2377T>C non_coding_transcript_exon_variant 3/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SNRKENST00000296088.12 linkuse as main transcriptc.1758A>G p.Pro586= synonymous_variant 7/71 NM_017719.5 P1Q9NRH2-1
SNRK-AS1ENST00000607513.2 linkuse as main transcriptn.896T>C non_coding_transcript_exon_variant 3/3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0269
AC:
4086
AN:
152142
Hom.:
188
Cov.:
32
show subpopulations
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
GnomAD3 exomes
AF:
0.00739
AC:
1809
AN:
244756
Hom.:
83
AF XY:
0.00587
AC XY:
782
AN XY:
133210
show subpopulations
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 SAS exome
AF:
0.0000991
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
show subpopulations
Gnomad4 AFR exome
AF:
0.0955
Gnomad4 AMR exome
AF:
0.00613
Gnomad4 ASJ exome
AF:
0.0113
Gnomad4 EAS exome
AF:
0.0000756
Gnomad4 SAS exome
AF:
0.0000698
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000329
Gnomad4 OTH exome
AF:
0.00730
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0269
AC:
4098
AN:
152260
Hom.:
189
Cov.:
32
AF XY:
0.0257
AC XY:
1912
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.0911
Gnomad4 AMR
AF:
0.0125
Gnomad4 ASJ
AF:
0.0101
Gnomad4 EAS
AF:
0.000387
Gnomad4 SAS
AF:
0.000415
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000529
Gnomad4 OTH
AF:
0.0213
Alfa
AF:
0.00894
Hom.:
30
Bravo
AF:
0.0314
Asia WGS
AF:
0.0110
AC:
37
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
Cadd
Benign
0.17
Dann
Benign
0.46
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs34730190; hg19: chr3-43389509; API