dbSNP rs3124: SLK:c.*3427A>C (chr10-104029147-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014720.4(SLK):c.*3427A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,148 control chromosomes in the GnomAD database, including 3,706 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.21 ( 3705 hom., cov: 32)

Exomes 𝑓: 0.50 ( 1 hom. )

Consequence

SLK
NM_014720.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.326

Publications

4 publications found

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]

SLK links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SLK	NM_014720.4 link	c.*3427A>C	3_prime_UTR_variant	Exon 19 of 19	ENST00000369755.4	NP_055535.2	Q9H2G2-1
SLK	NM_001304743.2 link	c.*3427A>C	3_prime_UTR_variant	Exon 18 of 18		NP_001291672.1	Q9H2G2-2
SLK	XM_011540401.4 link	c.*3427A>C	3_prime_UTR_variant	Exon 18 of 18		XP_011538703.1
SLK	XM_047426039.1 link	c.*3427A>C	3_prime_UTR_variant	Exon 17 of 17		XP_047281995.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLK	ENST00000369755.4 link	c.*3427A>C		3_prime_UTR_variant	Exon 19 of 19	1	NM_014720.4	ENSP00000358770.3		Q9H2G2-1
SLK	ENST00000335753.8 link	c.*3427A>C		3_prime_UTR_variant	Exon 18 of 18	1		ENSP00000336824.4		Q9H2G2-2

Frequencies

GnomAD3 genomes

AF:

0.209

AC:

31810

AN:

152026

Hom.:

3693

Cov.:

show subpopulations

Gnomad AFR

AF:

0.301

Gnomad AMI

AF:

0.290

Gnomad AMR

AF:

0.175

Gnomad ASJ

AF:

0.130

Gnomad EAS

AF:

0.0987

Gnomad SAS

AF:

0.178

Gnomad FIN

AF:

0.231

Gnomad MID

AF:

0.159

Gnomad NFE

AF:

0.172

Gnomad OTH

AF:

0.204

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.209

AC:

31874

AN:

152144

Hom.:

3705

Cov.:

AF XY:

0.210

AC XY:

15648

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.302

AC:

12523

AN:

41492

American (AMR)

AF:

0.175

AC:

2676

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.130

AC:

451

AN:

3472

East Asian (EAS)

AF:

0.0989

AC:

513

AN:

5186

South Asian (SAS)

AF:

0.178

AC:

861

AN:

4830

European-Finnish (FIN)

AF:

0.231

AC:

2442

AN:

10576

Middle Eastern (MID)

AF:

0.158

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.172

AC:

11672

AN:

67994

Other (OTH)

AF:

0.202

AC:

427

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1252

2504

3756

5008

6260

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

340

680

1020

1360

1700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.184

Hom.:

3456

Bravo

AF:

0.210

Asia WGS

AF:

0.156

AC:

543

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

8.7

(source)

DANN

Benign

0.78

PhyloP100

-0.33

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over