Variant chr13-98446628-A-C details in Genebe, Genetics Data Aggregator

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

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]

STK24 links:

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]

FARP1 links:

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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
STK24	NM_001032296.4 linkuse as main transcript	c.*6545T>G		3_prime_UTR_variant	11/11	ENST00000539966.6
FARP1	NM_005766.4 linkuse as main transcript	c.2905-38A>C		intron_variant		ENST00000319562.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK24	ENST00000539966.6 linkuse as main transcript	c.*6545T>G		3_prime_UTR_variant	11/11	1	NM_001032296.4	P1	Q9Y6E0-2
FARP1	ENST00000319562.11 linkuse as main transcript	c.2905-38A>C		intron_variant		1	NM_005766.4	P1	Q9Y4F1-1

Frequencies

GnomAD3 genomes

AF:

0.700

AC:

106267

AN:

151854

Hom.:

39025

Cov.:

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.:

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.:

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.

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