rs4130405

Variant names:

• chr8-98408547-A-C
• rs4130405
• XM_047422133.1:c.1424-20300T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-98408547-A-C
• chr8-98408547-A-G

Variant summary

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

The ENST00000517832.1(STK3):​n.484-7034T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,172 control chromosomes in the GnomAD database, including 2,711 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 0.15 (2711 hom., cov: 33)
• Consequence: STK3 ENST00000517832.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 10 publications found

Genes affected

STK3 (HGNC:11406): (serine/threonine kinase 3) This gene encodes a serine/threonine protein kinase activated by proapoptotic molecules indicating the encoded protein functions as a growth suppressor. Cleavage of the protein product by caspase removes the inhibitory C-terminal portion. The N-terminal portion is transported to the nucleus where it homodimerizes to form the active kinase which promotes the condensation of chromatin during apoptosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517832.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK3	ENST00000517832.1	TSL:3	n.484-7034T>G		intron	N/A
	STK3	ENST00000649151.1		n.428-20300T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22159 AN: 152056 Hom.: 2710 Cov.: 33

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0970

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.146 AC: 22153 AN: 152172 Hom.: 2711 Cov.: 33 AF XY: 0.150 AC XY: 11182 AN XY: 74400

African (AFR) AF: 0.0343 AC: 1424 AN: 41540

American (AMR) AF: 0.381 AC: 5822 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3470

East Asian (EAS) AF: 0.428 AC: 2211 AN: 5160

South Asian (SAS) AF: 0.126 AC: 608 AN: 4824

European-Finnish (FIN) AF: 0.0970 AC: 1028 AN: 10594

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9950 AN: 67990

Other (OTH) AF: 0.180 AC: 380 AN: 2112

Alfa AF: 0.127 Hom.: 1175

Bravo AF: 0.168

Asia WGS AF: 0.268 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	15
DANN	Benign	0.42
PhyloP100		1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4130405; hg19: chr8-99420775;