Variant 5-172054563-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_005990.4(STK10):c.2652+6G>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00398 in 1,603,658 control chromosomes in the GnomAD database, including 194 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.019 ( 93 hom., cov: 32)

Exomes 𝑓: 0.0024 ( 101 hom. )

Consequence

STK10
NM_005990.4 splice_region, intron

Scores

Splicing: ADA: 0.0004068

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.561

Variant links:

Genes affected

STK10 (HGNC:11388): (serine/threonine kinase 10) This gene encodes a member of the Ste20 family of serine/threonine protein kinases, and is similar to several known polo-like kinase kinases. The protein can associate with and phosphorylate polo-like kinase 1, and overexpression of a kinase-dead version of the protein interferes with normal cell cycle progression. The kinase can also negatively regulate interleukin 2 expression in T-cells via the mitogen activated protein kinase kinase 1 pathway. [provided by RefSeq, Jul 2008]

STK10 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 5-172054563-C-G is Benign according to our data. Variant chr5-172054563-C-G is described in ClinVar as [Benign]. Clinvar id is 788528.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
STK10	NM_005990.4 linkuse as main transcript	c.2652+6G>C	splice_region_variant, intron_variant	ENST00000176763.10	NP_005981.3	O94804
STK10	XM_047417627.1 linkuse as main transcript	c.2262+6G>C	splice_region_variant, intron_variant		XP_047273583.1
STK10	XM_047417628.1 linkuse as main transcript	c.2103+6G>C	splice_region_variant, intron_variant		XP_047273584.1
STK10	XM_047417629.1 linkuse as main transcript	c.1968+6G>C	splice_region_variant, intron_variant		XP_047273585.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK10	ENST00000176763.10 linkuse as main transcript	c.2652+6G>C		splice_region_variant, intron_variant		1	NM_005990.4	ENSP00000176763.5		O94804
STK10	ENST00000520476.1 linkuse as main transcript	c.468+6G>C		splice_region_variant, intron_variant		2		ENSP00000428806.1		H0YB71

Frequencies

GnomAD3 genomes

AF:

0.0187

AC:

2839

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0634

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00792

Gnomad ASJ

AF:

0.00750

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000426

Gnomad OTH

AF:

0.0163

GnomAD3 exomes

AF:

0.00565

AC:

1369

AN:

242108

Hom.:

AF XY:

0.00425

AC XY:

559

AN XY:

131416

show subpopulations

Gnomad AFR exome

AF:

0.0657

Gnomad AMR exome

AF:

0.00432

Gnomad ASJ exome

AF:

0.00676

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000198

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000681

Gnomad OTH exome

AF:

0.00303

GnomAD4 exome

AF:

0.00244

AC:

3541

AN:

1451386

Hom.:

101

Cov.:

AF XY:

0.00216

AC XY:

1558

AN XY:

722256

show subpopulations

Gnomad4 AFR exome

AF:

0.0690

Gnomad4 AMR exome

AF:

0.00498

Gnomad4 ASJ exome

AF:

0.00611

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000186

Gnomad4 FIN exome

AF:

0.0000445

Gnomad4 NFE exome

AF:

0.000391

Gnomad4 OTH exome

AF:

0.00625

GnomAD4 genome

AF:

0.0187

AC:

2846

AN:

152272

Hom.:

Cov.:

AF XY:

0.0176

AC XY:

1309

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0635

Gnomad4 AMR

AF:

0.00778

Gnomad4 ASJ

AF:

0.00750

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000426

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.00225

Hom.:

Bravo

AF:

0.0221

Asia WGS

AF:

0.00404

AC:

AN:

3478

EpiCase

AF:

0.00104

EpiControl

AF:

0.000833

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Oct 03, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

5.9

DANN

Benign

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00041

dbscSNV1_RF

Benign

0.12

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over