rs1993498

chr12-10646016-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018423.3(STYK1):c.-194-8820C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,034 control chromosomes in the GnomAD database, including 25,968 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 0.58 (25968 hom., cov: 32)
• Consequence: STYK1 NM_018423.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STYK1	NM_018423.3	c.-194-8820C>T		intron_variant		ENST00000075503.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STYK1	ENST00000075503.8	c.-194-8820C>T		intron_variant		1	NM_018423.3	P1

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87804 AN: 151918 Hom.: 25948 Cov.: 32

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.578 AC: 87865 AN: 152034 Hom.: 25968 Cov.: 32 AF XY: 0.589 AC XY: 43788 AN XY: 74332

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.602

Alfa AF: 0.581 Hom.: 3214

Bravo AF: 0.579

Asia WGS AF: 0.712 AC: 2474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	8.1
Dann	Benign	0.79

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

Other links and lift over

dbSNP: rs1993498; hg19: chr12-10798615;