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GeneBe

1-36355338-A-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001282547.2(STK40):c.438T>C(p.Ala146=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00249 in 1,614,178 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0024 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0025 ( 7 hom. )

Consequence

STK40
NM_001282547.2 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.29
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 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=-0.8).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 1-36355338-A-G is Benign according to our data. Variant chr1-36355338-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2638671.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=-2.29 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 359 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
STK40NM_001282547.2 linkuse as main transcriptc.438T>C p.Ala146= synonymous_variant 5/11 ENST00000373132.4
STK40NM_001282546.2 linkuse as main transcriptc.453T>C p.Ala151= synonymous_variant 5/11
STK40NM_032017.3 linkuse as main transcriptc.438T>C p.Ala146= synonymous_variant 6/12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
STK40ENST00000373132.4 linkuse as main transcriptc.438T>C p.Ala146= synonymous_variant 5/111 NM_001282547.2 A1Q8N2I9-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00236
AC:
359
AN:
152174
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000386
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00164
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00124
Gnomad FIN
AF:
0.0115
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00273
Gnomad OTH
AF:
0.00191
GnomAD3 exomes
AF:
0.00230
AC:
578
AN:
251488
Hom.:
3
AF XY:
0.00236
AC XY:
321
AN XY:
135920
show subpopulations
Gnomad AFR exome
AF:
0.000492
Gnomad AMR exome
AF:
0.00130
Gnomad ASJ exome
AF:
0.0000992
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00150
Gnomad FIN exome
AF:
0.00993
Gnomad NFE exome
AF:
0.00224
Gnomad OTH exome
AF:
0.00130
GnomAD4 exome
AF:
0.00250
AC:
3656
AN:
1461886
Hom.:
7
Cov.:
32
AF XY:
0.00240
AC XY:
1748
AN XY:
727242
show subpopulations
Gnomad4 AFR exome
AF:
0.000329
Gnomad4 AMR exome
AF:
0.00116
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00198
Gnomad4 FIN exome
AF:
0.00985
Gnomad4 NFE exome
AF:
0.00248
Gnomad4 OTH exome
AF:
0.00219
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00236
AC:
359
AN:
152292
Hom.:
0
Cov.:
32
AF XY:
0.00251
AC XY:
187
AN XY:
74464
show subpopulations
Gnomad4 AFR
AF:
0.000385
Gnomad4 AMR
AF:
0.00163
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00124
Gnomad4 FIN
AF:
0.0115
Gnomad4 NFE
AF:
0.00273
Gnomad4 OTH
AF:
0.00189
Alfa
AF:
0.00207
Hom.:
0
Bravo
AF:
0.00153
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.00185
EpiControl
AF:
0.00219

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 submitterclinical testingCeGaT Center for Human Genetics TuebingenApr 01, 2023STK40: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
Cadd
Benign
0.16
Dann
Benign
0.46

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: rs145965967; hg19: chr1-36820939; API