Variant 5-111394859-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001744.6(CAMK4):c.459+77C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.909 in 889,060 control chromosomes in the GnomAD database, including 368,231 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 0.91 ( 62913 hom., cov: 30)

Exomes 𝑓: 0.91 ( 305318 hom. )

Consequence

CAMK4
NM_001744.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.923

Variant links:

Genes affected

CAMK4 (HGNC:1464): (calcium/calmodulin dependent protein kinase IV) The product of this gene belongs to the serine/threonine protein kinase family, and to the Ca(2+)/calmodulin-dependent protein kinase subfamily. This enzyme is a multifunctional serine/threonine protein kinase with limited tissue distribution, that has been implicated in transcriptional regulation in lymphocytes, neurons and male germ cells. [provided by RefSeq, Jul 2008]

CAMK4 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK4	NM_001744.6 link	c.459+77C>T		intron_variant		ENST00000282356.9	NP_001735.1	Q16566

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK4	ENST00000282356.9 link	c.459+77C>T		intron_variant		1	NM_001744.6	ENSP00000282356.4		Q16566

Frequencies

GnomAD3 genomes

AF:

0.909

AC:

138125

AN:

151942

Hom.:

62868

Cov.:

show subpopulations

Gnomad AFR

AF:

0.917

Gnomad AMI

AF:

0.751

Gnomad AMR

AF:

0.908

Gnomad ASJ

AF:

0.933

Gnomad EAS

AF:

0.990

Gnomad SAS

AF:

0.979

Gnomad FIN

AF:

0.935

Gnomad MID

AF:

0.889

Gnomad NFE

AF:

0.890

Gnomad OTH

AF:

0.896

GnomAD4 exome

AF:

0.909

AC:

670236

AN:

737000

Hom.:

305318

AF XY:

0.912

AC XY:

357351

AN XY:

391658

show subpopulations

Gnomad4 AFR exome

AF:

0.916

Gnomad4 AMR exome

AF:

0.940

Gnomad4 ASJ exome

AF:

0.937

Gnomad4 EAS exome

AF:

0.991

Gnomad4 SAS exome

AF:

0.975

Gnomad4 FIN exome

AF:

0.927

Gnomad4 NFE exome

AF:

0.888

Gnomad4 OTH exome

AF:

0.903

GnomAD4 genome

AF:

0.909

AC:

138229

AN:

152060

Hom.:

62913

Cov.:

AF XY:

0.912

AC XY:

67744

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.917

Gnomad4 AMR

AF:

0.908

Gnomad4 ASJ

AF:

0.933

Gnomad4 EAS

AF:

0.990

Gnomad4 SAS

AF:

0.979

Gnomad4 FIN

AF:

0.935

Gnomad4 NFE

AF:

0.890

Gnomad4 OTH

AF:

0.897

Alfa

AF:

0.902

Hom.:

9459

Bravo

AF:

0.906

Asia WGS

AF:

0.972

AC:

3380

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.90

DANN

Benign

0.44

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