Variant 1-36344125-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001282547.2(STK40):c.879T>C(p.Ile293Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0045 in 1,536,460 control chromosomes in the GnomAD database, including 237 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.023 ( 122 hom., cov: 30)

Exomes 𝑓: 0.0026 ( 115 hom. )

Consequence

STK40
NM_001282547.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 3.29

Variant links:

Genes affected

STK40 (HGNC:21373): (serine/threonine kinase 40) Predicted to enable ATP binding activity; protein serine kinase activity; and protein serine/threonine kinase activity. Predicted to be involved in protein phosphorylation. Predicted to act upstream of or within several processes, including glycogen metabolic process; lung development; and respiratory system process. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

STK40 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 1-36344125-A-G is Benign according to our data. Variant chr1-36344125-A-G is described in ClinVar as [Benign]. Clinvar id is 783934.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=3.29 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK40	NM_001282547.2 linkuse as main transcript	c.879T>C	p.Ile293Ile	synonymous_variant	8/11	ENST00000373132.4	NP_001269476.1	Q8N2I9-1
STK40	NM_001282546.2 linkuse as main transcript	c.894T>C	p.Ile298Ile	synonymous_variant	8/11		NP_001269475.1	Q8N2I9-4
STK40	NM_032017.3 linkuse as main transcript	c.879T>C	p.Ile293Ile	synonymous_variant	9/12		NP_114406.1	Q8N2I9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
STK40	ENST00000373132.4 linkuse as main transcript	c.879T>C	p.Ile293Ile	synonymous_variant	8/11	1	NM_001282547.2	ENSP00000362224.4	Q8N2I9-1
STK40	ENST00000373130.7 linkuse as main transcript	c.894T>C	p.Ile298Ile	synonymous_variant	8/11	1		ENSP00000362222.3	Q8N2I9-4
STK40	ENST00000373129.7 linkuse as main transcript	c.879T>C	p.Ile293Ile	synonymous_variant	9/12	1		ENSP00000362221.3	Q8N2I9-1
STK40	ENST00000359297.6 linkuse as main transcript	c.879T>C	p.Ile293Ile	synonymous_variant	7/9	2		ENSP00000352245.2	Q8N2I9-3

Frequencies

GnomAD3 genomes

AF:

0.0231

AC:

3234

AN:

140166

Hom.:

123

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0820

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00884

Gnomad ASJ

AF:

0.00236

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00350

Gnomad NFE

AF:

0.000440

Gnomad OTH

AF:

0.0192

GnomAD3 exomes

AF:

0.00600

AC:

1466

AN:

244168

Hom.:

AF XY:

0.00440

AC XY:

582

AN XY:

132168

show subpopulations

Gnomad AFR exome

AF:

0.0754

Gnomad AMR exome

AF:

0.00377

Gnomad ASJ exome

AF:

0.00244

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000167

Gnomad FIN exome

AF:

0.0000474

Gnomad NFE exome

AF:

0.000579

Gnomad OTH exome

AF:

0.00525

GnomAD4 exome

AF:

0.00263

AC:

3671

AN:

1396224

Hom.:

115

Cov.:

AF XY:

0.00228

AC XY:

1581

AN XY:

694766

show subpopulations

Gnomad4 AFR exome

AF:

0.0826

Gnomad4 AMR exome

AF:

0.00521

Gnomad4 ASJ exome

AF:

0.00190

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000201

Gnomad4 FIN exome

AF:

0.0000210

Gnomad4 NFE exome

AF:

0.000304

Gnomad4 OTH exome

AF:

0.00697

GnomAD4 genome

AF:

0.0232

AC:

3250

AN:

140236

Hom.:

122

Cov.:

AF XY:

0.0236

AC XY:

1590

AN XY:

67510

show subpopulations

Gnomad4 AFR

AF:

0.0822

Gnomad4 AMR

AF:

0.00883

Gnomad4 ASJ

AF:

0.00236

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000440

Gnomad4 OTH

AF:

0.0191

Alfa

AF:

0.0102

Hom.:

Bravo

AF:

0.0250

Asia WGS

AF:

0.00549

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 14, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

7.9

DANN

Benign

0.74

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