Variant 7-23754334-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_031414.5(STK31):c.1153C>T(p.Arg385Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00534 in 1,609,966 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0058 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0053 ( 34 hom. )

Consequence

STK31
NM_031414.5 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.50

Variant links:

Genes affected

STK31 (HGNC:11407): (serine/threonine kinase 31) This gene is similar to a mouse gene that encodes a putative protein kinase with a tudor domain, and shows testis-specific expression. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

STK31 links:

STK31 (HGNC:):

STK31 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.009837657).

BP6

Variant 7-23754334-C-T is Benign according to our data. Variant chr7-23754334-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2657352.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00529 (7716/1457830) while in subpopulation MID AF= 0.0182 (105/5758). AF 95% confidence interval is 0.0154. There are 34 homozygotes in gnomad4_exome. There are 3955 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK31	NM_031414.5 linkuse as main transcript	c.1153C>T	p.Arg385Cys	missense_variant	10/24	ENST00000355870.8	NP_113602.2	Q9BXU1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK31	ENST00000355870.8 linkuse as main transcript	c.1153C>T	p.Arg385Cys	missense_variant	10/24	1	NM_031414.5	ENSP00000348132.3		Q9BXU1-1

Frequencies

GnomAD3 genomes

AF:

0.00580

AC:

882

AN:

152016

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00667

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00544

Gnomad ASJ

AF:

0.00692

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00601

Gnomad FIN

AF:

0.00123

Gnomad MID

AF:

0.0478

Gnomad NFE

AF:

0.00634

Gnomad OTH

AF:

0.00527

GnomAD3 exomes

AF:

0.00579

AC:

1432

AN:

247452

Hom.:

AF XY:

0.00610

AC XY:

815

AN XY:

133502

show subpopulations

Gnomad AFR exome

AF:

0.00704

Gnomad AMR exome

AF:

0.00392

Gnomad ASJ exome

AF:

0.00593

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00650

Gnomad FIN exome

AF:

0.00176

Gnomad NFE exome

AF:

0.00766

Gnomad OTH exome

AF:

0.00595

GnomAD4 exome

AF:

0.00529

AC:

7716

AN:

1457830

Hom.:

Cov.:

AF XY:

0.00546

AC XY:

3955

AN XY:

724892

show subpopulations

Gnomad4 AFR exome

AF:

0.00715

Gnomad4 AMR exome

AF:

0.00445

Gnomad4 ASJ exome

AF:

0.00581

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00615

Gnomad4 FIN exome

AF:

0.00240

Gnomad4 NFE exome

AF:

0.00540

Gnomad4 OTH exome

AF:

0.00632

GnomAD4 genome

AF:

0.00577

AC:

878

AN:

152136

Hom.:

Cov.:

AF XY:

0.00528

AC XY:

393

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.00663

Gnomad4 AMR

AF:

0.00544

Gnomad4 ASJ

AF:

0.00692

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00560

Gnomad4 FIN

AF:

0.00123

Gnomad4 NFE

AF:

0.00634

Gnomad4 OTH

AF:

0.00522

Alfa

AF:

0.00685

Hom.:

Bravo

AF:

0.00642

TwinsUK

AF:

0.00324

AC:

ALSPAC

AF:

0.00441

AC:

ESP6500AA

AF:

0.00704

AC:

ESP6500EA

AF:

0.00558

AC:

ExAC

AF:

0.00681

AC:

827

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.00887

EpiControl

AF:

0.00903

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

STK31: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.081

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.51

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0025

T;.;.

Eigen

Uncertain

0.20

Eigen_PC

Benign

0.15

FATHMM_MKL

Benign

0.72

LIST_S2

Benign

0.81

T;T;T

MetaRNN

Benign

0.0098

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.6

M;M;.

PrimateAI

Benign

0.29

PROVEAN

Benign

-1.9

N;N;N

REVEL

Benign

0.093

Sift

Uncertain

0.013

D;D;D

Sift4G

Uncertain

0.015

D;D;D

Polyphen

1.0

D;.;.

Vest4

0.34

MVP

0.55

MPC

0.076

ClinPred

0.033

GERP RS

4.0

Varity_R

0.090

gMVP

0.20

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

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