Variant rs1469000 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_031414.5(STK31):c.1714-19T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 1,600,556 control chromosomes in the GnomAD database, including 205,611 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 0.46 ( 16814 hom., cov: 32)

Exomes 𝑓: 0.51 ( 188797 hom. )

Consequence

STK31
NM_031414.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.621

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK31	NM_031414.5 link	c.1714-19T>C		intron_variant		ENST00000355870.8	NP_113602.2	Q9BXU1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK31	ENST00000355870.8 link	c.1714-19T>C		intron_variant		1	NM_031414.5	ENSP00000348132.3		Q9BXU1-1

Frequencies

GnomAD3 genomes

AF:

0.464

AC:

70473

AN:

151868

Hom.:

16801

Cov.:

show subpopulations

Gnomad AFR

AF:

0.375

Gnomad AMI

AF:

0.520

Gnomad AMR

AF:

0.549

Gnomad ASJ

AF:

0.424

Gnomad EAS

AF:

0.386

Gnomad SAS

AF:

0.538

Gnomad FIN

AF:

0.448

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.504

Gnomad OTH

AF:

0.458

GnomAD3 exomes

AF:

0.497

AC:

119519

AN:

240576

Hom.:

30797

AF XY:

0.495

AC XY:

64326

AN XY:

129878

show subpopulations

Gnomad AFR exome

AF:

0.363

Gnomad AMR exome

AF:

0.642

Gnomad ASJ exome

AF:

0.435

Gnomad EAS exome

AF:

0.349

Gnomad SAS exome

AF:

0.530

Gnomad FIN exome

AF:

0.453

Gnomad NFE exome

AF:

0.503

Gnomad OTH exome

AF:

0.495

GnomAD4 exome

AF:

0.508

AC:

735890

AN:

1448570

Hom.:

188797

Cov.:

AF XY:

0.508

AC XY:

365813

AN XY:

720422

show subpopulations

Gnomad4 AFR exome

AF:

0.370

Gnomad4 AMR exome

AF:

0.628

Gnomad4 ASJ exome

AF:

0.431

Gnomad4 EAS exome

AF:

0.455

Gnomad4 SAS exome

AF:

0.529

Gnomad4 FIN exome

AF:

0.456

Gnomad4 NFE exome

AF:

0.514

Gnomad4 OTH exome

AF:

0.483

GnomAD4 genome

AF:

0.464

AC:

70524

AN:

151986

Hom.:

16814

Cov.:

AF XY:

0.465

AC XY:

34525

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.375

Gnomad4 AMR

AF:

0.549

Gnomad4 ASJ

AF:

0.424

Gnomad4 EAS

AF:

0.386

Gnomad4 SAS

AF:

0.541

Gnomad4 FIN

AF:

0.448

Gnomad4 NFE

AF:

0.504

Gnomad4 OTH

AF:

0.455

Alfa

AF:

0.494

Hom.:

9724

Bravo

AF:

0.465

Asia WGS

AF:

0.469

AC:

1636

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

9.8

DANN

Benign

0.75

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over