12-10653686-T-C

Variant names:

• chr12-10653686-T-C
• rs2418087
• NM_018423.3:c.-194-16490A>G

Variant summary

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

The NM_018423.3(STYK1):​c.-194-16490A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,084 control chromosomes in the GnomAD database, including 9,159 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 0.33 (9159 hom., cov: 32)
• Consequence: STYK1 NM_018423.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STYK1	NM_018423.3	c.-194-16490A>G		intron_variant	Intron 1 of 10	ENST00000075503.8	NP_060893.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STYK1	ENST00000075503.8	c.-194-16490A>G		intron_variant	Intron 1 of 10	1	NM_018423.3	ENSP00000075503.3

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49888 AN: 151966 Hom.: 9161 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.328 AC: 49896 AN: 152084 Hom.: 9159 Cov.: 32 AF XY: 0.319 AC XY: 23752 AN XY: 74342

African (AFR) AF: 0.167 AC: 6945 AN: 41526

American (AMR) AF: 0.287 AC: 4387 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1392 AN: 3470

East Asian (EAS) AF: 0.205 AC: 1060 AN: 5166

South Asian (SAS) AF: 0.330 AC: 1592 AN: 4822

European-Finnish (FIN) AF: 0.362 AC: 3817 AN: 10546

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29379 AN: 67948

Other (OTH) AF: 0.345 AC: 730 AN: 2116

Alfa AF: 0.400 Hom.: 8117

Bravo AF: 0.313

Asia WGS AF: 0.257 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.46
PhyloP100		1.0
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: rs2418087; hg19: chr12-10806285;