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GeneBe

10-104002885-G-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_014720.4(SLK):c.1707G>T(p.Thr569=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00307 in 1,614,076 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0020 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0032 ( 12 hom. )

Consequence

SLK
NM_014720.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.177
Variant links:
Genes affected
SLK (HGNC:11088): (STE20 like kinase) Enables protein homodimerization activity and protein serine/threonine kinase activity. Involved in several processes, including cytoplasmic microtubule organization; protein autophosphorylation; and regulation of focal adhesion assembly. Located in perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 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=-0.83).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 10-104002885-G-T is Benign according to our data. Variant chr10-104002885-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2640812.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=-0.177 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 310 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLKNM_014720.4 linkuse as main transcriptc.1707G>T p.Thr569= synonymous_variant 9/19 ENST00000369755.4
SLKNM_001304743.2 linkuse as main transcriptc.1707G>T p.Thr569= synonymous_variant 9/18
SLKXM_011540401.4 linkuse as main transcriptc.993+1313G>T intron_variant
SLKXM_047426039.1 linkuse as main transcriptc.993+1313G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLKENST00000369755.4 linkuse as main transcriptc.1707G>T p.Thr569= synonymous_variant 9/191 NM_014720.4 P1Q9H2G2-1
SLKENST00000335753.8 linkuse as main transcriptc.1707G>T p.Thr569= synonymous_variant 9/181 Q9H2G2-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00204
AC:
310
AN:
152172
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000507
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00164
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00186
Gnomad FIN
AF:
0.0000943
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00363
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00198
AC:
498
AN:
251184
Hom.:
1
AF XY:
0.00216
AC XY:
293
AN XY:
135768
show subpopulations
Gnomad AFR exome
AF:
0.000616
Gnomad AMR exome
AF:
0.000724
Gnomad ASJ exome
AF:
0.000496
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00141
Gnomad FIN exome
AF:
0.000278
Gnomad NFE exome
AF:
0.00352
Gnomad OTH exome
AF:
0.00147
GnomAD4 exome
AF:
0.00318
AC:
4647
AN:
1461786
Hom.:
12
Cov.:
33
AF XY:
0.00310
AC XY:
2252
AN XY:
727186
show subpopulations
Gnomad4 AFR exome
AF:
0.000478
Gnomad4 AMR exome
AF:
0.000827
Gnomad4 ASJ exome
AF:
0.000344
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00115
Gnomad4 FIN exome
AF:
0.000543
Gnomad4 NFE exome
AF:
0.00386
Gnomad4 OTH exome
AF:
0.00268
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00204
AC:
310
AN:
152290
Hom.:
1
Cov.:
32
AF XY:
0.00179
AC XY:
133
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.000505
Gnomad4 AMR
AF:
0.00163
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00187
Gnomad4 FIN
AF:
0.0000943
Gnomad4 NFE
AF:
0.00363
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00266
Hom.:
0
Bravo
AF:
0.00210
EpiCase
AF:
0.00349
EpiControl
AF:
0.00362

ClinVar

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

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2022SLK: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
0.28
Dann
Benign
0.39
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs56357599; hg19: chr10-105762643; API