dbSNP rs12304656: STYK1:c.633+124G>C (chr12-10629369-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_018423.3(STYK1):c.633+124G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0135 in 973,432 control chromosomes in the GnomAD database, including 906 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 0.048 ( 566 hom., cov: 33)

Exomes 𝑓: 0.0071 ( 340 hom. )

Consequence

STYK1
NM_018423.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0880

Publications

2 publications found

Variant links:

Genes affected

STYK1 (HGNC:18889): (serine/threonine/tyrosine kinase 1) Receptor protein tyrosine kinases, like STYK1, play important roles in diverse cellular and developmental processes, such as cell proliferation, differentiation, and survival (Liu et al., 2004 [PubMed 15150103]).[supplied by OMIM, Mar 2008]

STYK1 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STYK1	NM_018423.3 link	c.633+124G>C		intron_variant	Intron 6 of 10	ENST00000075503.8	NP_060893.2	Q6J9G0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STYK1	ENST00000075503.8 link	c.633+124G>C		intron_variant	Intron 6 of 10	1	NM_018423.3	ENSP00000075503.3		Q6J9G0
STYK1	ENST00000542924.1 link	c.162+106G>C		intron_variant	Intron 1 of 1	2		ENSP00000443760.1		H0YGL5

Frequencies

GnomAD3 genomes

AF:

0.0474

AC:

7211

AN:

152072

Hom.:

560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0222

Gnomad ASJ

AF:

0.0156

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.00869

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0573

Gnomad NFE

AF:

0.00104

Gnomad OTH

AF:

0.0306

GnomAD4 exome

AF:

0.00713

AC:

5856

AN:

821242

Hom.:

340

AF XY:

0.00659

AC XY:

2758

AN XY:

418572

show subpopulations

African (AFR)

AF:

0.173

AC:

3554

AN:

20556

American (AMR)

AF:

0.0115

AC:

333

AN:

28894

Ashkenazi Jewish (ASJ)

AF:

0.0160

AC:

299

AN:

18658

East Asian (EAS)

AF:

0.00220

AC:

AN:

32734

South Asian (SAS)

AF:

0.00554

AC:

328

AN:

59240

European-Finnish (FIN)

AF:

0.00

AC:

AN:

42678

Middle Eastern (MID)

AF:

0.0392

AC:

109

AN:

2780

European-Non Finnish (NFE)

AF:

0.000883

AC:

510

AN:

577266

Other (OTH)

AF:

0.0169

AC:

651

AN:

38436

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

263

526

790

1053

1316

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

108

216

324

432

540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0476

AC:

7244

AN:

152190

Hom.:

566

Cov.:

AF XY:

0.0473

AC XY:

3523

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.160

AC:

6647

AN:

41486

American (AMR)

AF:

0.0222

AC:

339

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0156

AC:

AN:

3468

East Asian (EAS)

AF:

0.00231

AC:

AN:

5190

South Asian (SAS)

AF:

0.00829

AC:

AN:

4828

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10582

Middle Eastern (MID)

AF:

0.0582

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00104

AC:

AN:

68030

Other (OTH)

AF:

0.0302

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

317

634

951

1268

1585

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

198

264

330

<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:

0.0356

Hom.:

Bravo

AF:

0.0531

Asia WGS

AF:

0.0200

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.5

(source)

DANN

Benign

0.42

PhyloP100

-0.088

PromoterAI

0.00030

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over