chr13-98458955-G-C

Variant names:

• chr13-98458955-G-C
• rs3783006
• NM_001032296.4:c.1122+1417C>G

Variant summary

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

The NM_001032296.4(STK24):​c.1122+1417C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 152,102 control chromosomes in the GnomAD database, including 12,198 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 0.40 (12198 hom., cov: 33)
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 11 publications found

Genes affected

STK24 (HGNC:11403): (serine/threonine kinase 24) This gene encodes a serine/threonine protein kinase that functions upstream of mitogen-activated protein kinase (MAPK) signaling. The encoded protein is cleaved into two chains by caspases; the N-terminal fragment (MST3/N) translocates to the nucleus and promotes programmed cells death. There is a pseudogene for this gene on chromosome X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001032296.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK24	NM_001032296.4	MANE Select	c.1122+1417C>G		intron	N/A	NP_001027467.2
	STK24	NM_003576.5		c.1158+1417C>G		intron	N/A	NP_003567.2
	STK24	NM_001286649.2		c.1065+1417C>G		intron	N/A	NP_001273578.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK24	ENST00000539966.6	TSL:1 MANE Select	c.1122+1417C>G		intron	N/A	ENSP00000442539.2
	STK24	ENST00000376547.7	TSL:1	c.1158+1417C>G		intron	N/A	ENSP00000365730.3
	STK24	ENST00000444574.1	TSL:1	c.873+1417C>G		intron	N/A	ENSP00000402764.1

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60098 AN: 151984 Hom.: 12181 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.396 AC: 60159 AN: 152102 Hom.: 12198 Cov.: 33 AF XY: 0.390 AC XY: 28968 AN XY: 74354

African (AFR) AF: 0.325 AC: 13488 AN: 41510

American (AMR) AF: 0.381 AC: 5831 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1553 AN: 3464

East Asian (EAS) AF: 0.309 AC: 1594 AN: 5154

South Asian (SAS) AF: 0.379 AC: 1823 AN: 4816

European-Finnish (FIN) AF: 0.329 AC: 3472 AN: 10568

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30912 AN: 67984

Other (OTH) AF: 0.426 AC: 901 AN: 2114

Alfa AF: 0.437 Hom.: 1867

Bravo AF: 0.395

Asia WGS AF: 0.360 AC: 1254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.52
PhyloP100		-0.64
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: rs3783006; hg19: chr13-99111209;