rs7968536

chr12-10665645-A-G

Variant summary

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

The NM_018423.3(STYK1):c.-195+8321T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,108 control chromosomes in the GnomAD database, including 8,316 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 0.30 (8316 hom., cov: 33)
• Consequence: STYK1 NM_018423.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STYK1	NM_018423.3	c.-195+8321T>C		intron_variant		ENST00000075503.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STYK1	ENST00000075503.8	c.-195+8321T>C		intron_variant		1	NM_018423.3	P1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45481 AN: 151990 Hom.: 8288 Cov.: 33

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.300 AC: 45560 AN: 152108 Hom.: 8316 Cov.: 33 AF XY: 0.297 AC XY: 22123 AN XY: 74364

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.311

Alfa AF: 0.238 Hom.: 9448

Bravo AF: 0.308

Asia WGS AF: 0.214 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	4.0
Dann	Benign	0.80

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: rs7968536; hg19: chr12-10818244;