rs2281766

Variant summary

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

The NM_001032296.4(STK24):​c.*6545T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.784 in 1,606,864 control chromosomes in the GnomAD database, including 503,237 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 0.70 ( 39033 hom., cov: 32)
Exomes 𝑓: 0.79 ( 464204 hom. )

Consequence

STK24
NM_001032296.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.305
Variant links:
Genes affected
STK24 (HGNC:11403): (serine/threonine kinase 24) This gene encodes a serine/threonine protein kinase that functions upstream of mitogen-activated protein kinase (MAPK) signaling. The encoded protein is cleaved into two chains by caspases; the N-terminal fragment (MST3/N) translocates to the nucleus and promotes programmed cells death. There is a pseudogene for this gene on chromosome X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]
FARP1 (HGNC:3591): (FERM, ARH/RhoGEF and pleckstrin domain protein 1) This gene encodes a protein containing a FERM (4.2, exrin, radixin, moesin) domain, a Dbl homology domain, and two pleckstrin homology domains. These domains are found in guanine nucleotide exchange factors and proteins that link the cytoskeleton to the cell membrane. The encoded protein functions in neurons to promote dendritic growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
STK24NM_001032296.4 linkuse as main transcriptc.*6545T>G 3_prime_UTR_variant 11/11 ENST00000539966.6
FARP1NM_005766.4 linkuse as main transcriptc.2905-38A>C intron_variant ENST00000319562.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
STK24ENST00000539966.6 linkuse as main transcriptc.*6545T>G 3_prime_UTR_variant 11/111 NM_001032296.4 P1Q9Y6E0-2
FARP1ENST00000319562.11 linkuse as main transcriptc.2905-38A>C intron_variant 1 NM_005766.4 P1Q9Y4F1-1

Frequencies

GnomAD3 genomes
AF:
0.700
AC:
106267
AN:
151854
Hom.:
39025
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.485
Gnomad AMI
AF:
0.944
Gnomad AMR
AF:
0.649
Gnomad ASJ
AF:
0.747
Gnomad EAS
AF:
0.627
Gnomad SAS
AF:
0.569
Gnomad FIN
AF:
0.843
Gnomad MID
AF:
0.631
Gnomad NFE
AF:
0.829
Gnomad OTH
AF:
0.694
GnomAD3 exomes
AF:
0.720
AC:
178081
AN:
247494
Hom.:
66434
AF XY:
0.725
AC XY:
96916
AN XY:
133766
show subpopulations
Gnomad AFR exome
AF:
0.478
Gnomad AMR exome
AF:
0.570
Gnomad ASJ exome
AF:
0.749
Gnomad EAS exome
AF:
0.613
Gnomad SAS exome
AF:
0.579
Gnomad FIN exome
AF:
0.844
Gnomad NFE exome
AF:
0.828
Gnomad OTH exome
AF:
0.746
GnomAD4 exome
AF:
0.793
AC:
1153314
AN:
1454892
Hom.:
464204
Cov.:
32
AF XY:
0.787
AC XY:
569469
AN XY:
723236
show subpopulations
Gnomad4 AFR exome
AF:
0.470
Gnomad4 AMR exome
AF:
0.576
Gnomad4 ASJ exome
AF:
0.749
Gnomad4 EAS exome
AF:
0.647
Gnomad4 SAS exome
AF:
0.584
Gnomad4 FIN exome
AF:
0.842
Gnomad4 NFE exome
AF:
0.833
Gnomad4 OTH exome
AF:
0.765
GnomAD4 genome
AF:
0.700
AC:
106308
AN:
151972
Hom.:
39033
Cov.:
32
AF XY:
0.697
AC XY:
51737
AN XY:
74270
show subpopulations
Gnomad4 AFR
AF:
0.486
Gnomad4 AMR
AF:
0.648
Gnomad4 ASJ
AF:
0.747
Gnomad4 EAS
AF:
0.626
Gnomad4 SAS
AF:
0.569
Gnomad4 FIN
AF:
0.843
Gnomad4 NFE
AF:
0.829
Gnomad4 OTH
AF:
0.693
Alfa
AF:
0.735
Hom.:
5106
Bravo
AF:
0.675
Asia WGS
AF:
0.615
AC:
2138
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
4.4
DANN
Benign
0.79

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: rs2281766; hg19: chr13-99098882; COSMIC: COSV60330386; COSMIC: COSV60330386; API