13-98463584-TAAAAA-TAAAA

Variant names:

• chr13-98463584-TA-T
• rs56325686
• NM_001032296.4:c.929+106delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001032296.4(STK24):​c.929+106delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.92 (61163 hom., cov: 0)
  • Exomes 𝑓: 0.51 (10878 hom.)
  • Failed GnomAD Quality Control
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 0 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.98 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.929+106delT		intron	N/A	NP_001027467.2
	STK24	NM_003576.5		c.965+106delT		intron	N/A	NP_003567.2
	STK24	NM_001286649.2		c.872+106delT		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.929+106delT		intron	N/A	ENSP00000442539.2
	STK24	ENST00000376547.7	TSL:1	c.965+106delT		intron	N/A	ENSP00000365730.3
	STK24	ENST00000444574.1	TSL:1	c.680+106delT		intron	N/A	ENSP00000402764.1

Frequencies

GnomAD3 genomes AF: 0.924 AC: 131569 AN: 142458 Hom.: 61167 Cov.: 0

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.975

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.970

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.935

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.507 AC: 459705 AN: 906260 Hom.: 10878 AF XY: 0.507 AC XY: 226575 AN XY: 447022

African (AFR) AF: 0.460 AC: 9773 AN: 21250

American (AMR) AF: 0.500 AC: 7826 AN: 15646

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 7455 AN: 14812

East Asian (EAS) AF: 0.502 AC: 14237 AN: 28350

South Asian (SAS) AF: 0.500 AC: 23926 AN: 47842

European-Finnish (FIN) AF: 0.508 AC: 13040 AN: 25690

Middle Eastern (MID) AF: 0.647 AC: 2646 AN: 4088

European-Non Finnish (NFE) AF: 0.509 AC: 360887 AN: 709182

Other (OTH) AF: 0.505 AC: 19915 AN: 39400

GnomAD4 genome AF: 0.923 AC: 131577 AN: 142490 Hom.: 61163 Cov.: 0 AF XY: 0.923 AC XY: 63625 AN XY: 68948

African (AFR) AF: 0.776 AC: 29995 AN: 38632

American (AMR) AF: 0.961 AC: 13865 AN: 14432

Ashkenazi Jewish (ASJ) AF: 0.978 AC: 3319 AN: 3394

East Asian (EAS) AF: 0.986 AC: 4823 AN: 4892

South Asian (SAS) AF: 0.975 AC: 4341 AN: 4452

European-Finnish (FIN) AF: 0.951 AC: 7850 AN: 8258

Middle Eastern (MID) AF: 0.967 AC: 265 AN: 274

European-Non Finnish (NFE) AF: 0.986 AC: 64402 AN: 65310

Other (OTH) AF: 0.934 AC: 1818 AN: 1946

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.2
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: rs56325686; hg19: chr13-99115838;