rs4763212

Variant names:

• chr12-10625967-C-A
• rs4763212
• NM_018423.3:c.718-1108G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-10625967-C-A
• chr12-10625967-C-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.718-1108G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.892 in 152,150 control chromosomes in the GnomAD database, including 62,486 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 0.89 (62486 hom., cov: 31)
• Consequence: STYK1 NM_018423.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STYK1	NM_018423.3	c.718-1108G>T		intron_variant	Intron 7 of 10	ENST00000075503.8	NP_060893.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STYK1	ENST00000075503.8	c.718-1108G>T		intron_variant	Intron 7 of 10	1	NM_018423.3	ENSP00000075503.3

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135629 AN: 152032 Hom.: 62473 Cov.: 31

Gnomad AFR AF: 0.629

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.991

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.892 AC: 135681 AN: 152150 Hom.: 62486 Cov.: 31 AF XY: 0.895 AC XY: 66618 AN XY: 74408

African (AFR) AF: 0.629 AC: 26034 AN: 41414

American (AMR) AF: 0.956 AC: 14620 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3418 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5158 AN: 5170

South Asian (SAS) AF: 0.991 AC: 4781 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10622 AN: 10622

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.998 AC: 67905 AN: 68032

Other (OTH) AF: 0.926 AC: 1958 AN: 2114

Alfa AF: 0.926 Hom.: 9321

Bravo AF: 0.878

Asia WGS AF: 0.967 AC: 3363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.084
DANN	Benign	0.48
PhyloP100		-1.3
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: rs4763212; hg19: chr12-10778566;