rs10492349

Variant names:

• chr12-10638229-A-G
• rs10492349
• NM_018423.3:c.-194-1033T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018423.3(STYK1):​c.-194-1033T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,192 control chromosomes in the GnomAD database, including 3,943 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 (3943 hom., cov: 32)
• Consequence: STYK1 NM_018423.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436
• Publications: 9 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018423.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STYK1	NM_018423.3	MANE Select	c.-194-1033T>C		intron	N/A	NP_060893.2	Q6J9G0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STYK1	ENST00000075503.8	TSL:1 MANE Select	c.-194-1033T>C		intron	N/A	ENSP00000075503.3	Q6J9G0
	STYK1	ENST00000954952.1		c.-194-1033T>C		intron	N/A	ENSP00000625011.1
	STYK1	ENST00000878937.1		c.-194-1033T>C		intron	N/A	ENSP00000548996.1

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32683 AN: 152074 Hom.: 3946 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.0949

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.244

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.215 AC: 32681 AN: 152192 Hom.: 3943 Cov.: 32 AF XY: 0.218 AC XY: 16198 AN XY: 74400

African (AFR) AF: 0.113 AC: 4712 AN: 41530

American (AMR) AF: 0.238 AC: 3644 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1256 AN: 3466

East Asian (EAS) AF: 0.0943 AC: 489 AN: 5184

South Asian (SAS) AF: 0.269 AC: 1297 AN: 4822

European-Finnish (FIN) AF: 0.235 AC: 2485 AN: 10584

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17996 AN: 67994

Other (OTH) AF: 0.240 AC: 507 AN: 2112

Alfa AF: 0.253 Hom.: 2855

Bravo AF: 0.208

Asia WGS AF: 0.151 AC: 523 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.73
PhyloP100		0.44
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10492349; hg19: chr12-10790828;