Menu
GeneBe

1-36341962-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001282547.2(STK40):c.1101G>A(p.Thr367=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0056 in 1,613,106 control chromosomes in the GnomAD database, including 114 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.017 ( 57 hom., cov: 33)
Exomes 𝑓: 0.0044 ( 57 hom. )

Consequence

STK40
NM_001282547.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -7.35
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-36341962-C-T is Benign according to our data. Variant chr1-36341962-C-T is described in ClinVar as [Benign]. Clinvar id is 783933.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-7.35 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0509 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
STK40NM_001282547.2 linkuse as main transcriptc.1101G>A p.Thr367= synonymous_variant 11/11 ENST00000373132.4
STK40NM_001282546.2 linkuse as main transcriptc.1116G>A p.Thr372= synonymous_variant 11/11
STK40NM_032017.3 linkuse as main transcriptc.1101G>A p.Thr367= synonymous_variant 12/12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
STK40ENST00000373132.4 linkuse as main transcriptc.1101G>A p.Thr367= synonymous_variant 11/111 NM_001282547.2 A1Q8N2I9-1
STK40ENST00000373130.7 linkuse as main transcriptc.1116G>A p.Thr372= synonymous_variant 11/111 P4Q8N2I9-4
STK40ENST00000373129.7 linkuse as main transcriptc.1101G>A p.Thr367= synonymous_variant 12/121 A1Q8N2I9-1
STK40ENST00000359297.6 linkuse as main transcriptc.*1237G>A 3_prime_UTR_variant 9/92 Q8N2I9-3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0172
AC:
2613
AN:
152258
Hom.:
59
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0512
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0124
Gnomad ASJ
AF:
0.0112
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.00329
Gnomad OTH
AF:
0.0167
GnomAD3 exomes
AF:
0.00690
AC:
1694
AN:
245568
Hom.:
22
AF XY:
0.00571
AC XY:
762
AN XY:
133338
show subpopulations
Gnomad AFR exome
AF:
0.0518
Gnomad AMR exome
AF:
0.00817
Gnomad ASJ exome
AF:
0.00901
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000756
Gnomad FIN exome
AF:
0.000282
Gnomad NFE exome
AF:
0.00367
Gnomad OTH exome
AF:
0.0113
GnomAD4 exome
AF:
0.00438
AC:
6402
AN:
1460730
Hom.:
57
Cov.:
31
AF XY:
0.00411
AC XY:
2987
AN XY:
726636
show subpopulations
Gnomad4 AFR exome
AF:
0.0530
Gnomad4 AMR exome
AF:
0.00866
Gnomad4 ASJ exome
AF:
0.00835
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000789
Gnomad4 FIN exome
AF:
0.000375
Gnomad4 NFE exome
AF:
0.00306
Gnomad4 OTH exome
AF:
0.00802
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0172
AC:
2625
AN:
152376
Hom.:
57
Cov.:
33
AF XY:
0.0172
AC XY:
1280
AN XY:
74510
show subpopulations
Gnomad4 AFR
AF:
0.0513
Gnomad4 AMR
AF:
0.0123
Gnomad4 ASJ
AF:
0.0112
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00331
Gnomad4 OTH
AF:
0.0166
Alfa
AF:
0.0110
Hom.:
21
Bravo
AF:
0.0191
Asia WGS
AF:
0.00520
AC:
18
AN:
3478
EpiCase
AF:
0.00480
EpiControl
AF:
0.00500

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 submitterclinical testingInvitaeDec 14, 2017- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
Cadd
Benign
0.034
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.

Other links and lift over

dbSNP: rs56405327; hg19: chr1-36807563; API