5-111295567-T-C

Variant names:

• chr5-111295567-T-C
• rs306104
• NM_001744.6:c.162-48457T>C

Variant summary

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

The NM_001744.6(CAMK4):​c.162-48457T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 151,990 control chromosomes in the GnomAD database, including 26,551 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 0.57 (26551 hom., cov: 32)
• Consequence: CAMK4 NM_001744.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.754

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]

ENSG00000248268 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMK4	NM_001744.6	c.162-48457T>C		intron_variant	Intron 1 of 10	ENST00000282356.9	NP_001735.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMK4	ENST00000282356.9	c.162-48457T>C		intron_variant	Intron 1 of 10	1	NM_001744.6	ENSP00000282356.4

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87181 AN: 151872 Hom.: 26554 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.574 AC: 87191 AN: 151990 Hom.: 26551 Cov.: 32 AF XY: 0.575 AC XY: 42683 AN XY: 74280

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.610

Alfa AF: 0.646 Hom.: 43622

Bravo AF: 0.569

Asia WGS AF: 0.609 AC: 2120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.8
DANN	Benign	0.73

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: rs306104; hg19: chr5-110631265;