rs2300782

Positions:

• chr5-111453087-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001744.6(CAMK4):​c.625+3884C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,036 control chromosomes in the GnomAD database, including 10,478 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 0.35 (10478 hom., cov: 32)
• Consequence: CAMK4 NM_001744.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK4	NM_001744.6	c.625+3884C>T		intron_variant		ENST00000282356.9	NP_001735.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK4	ENST00000282356.9	c.625+3884C>T		intron_variant		1	NM_001744.6	ENSP00000282356	P1

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52794 AN: 151918 Hom.: 10481 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.372

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.347 AC: 52794 AN: 152036 Hom.: 10478 Cov.: 32 AF XY: 0.348 AC XY: 25893 AN XY: 74310

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.370

Alfa AF: 0.380 Hom.: 1470

Bravo AF: 0.334

Asia WGS AF: 0.378 AC: 1314 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.45
DANN	Benign	0.68

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

Other links and lift over

dbSNP: rs2300782; hg19: chr5-110788785; COSMIC: COSV56666939; COSMIC: COSV56666939;