rs2399849

Positions:

• chr10-12457861-G-A

Variant summary

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

The NM_153498.4(CAMK1D):​c.93-95364G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,700 control chromosomes in the GnomAD database, including 2,689 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 0.18 (2689 hom., cov: 31)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

CAMK1D (HGNC:19341): (calcium/calmodulin dependent protein kinase ID) This gene is a member of the calcium/calmodulin-dependent protein kinase 1 family, a subfamily of the serine/threonine kinases. The encoded protein is a component of the calcium-regulated calmodulin-dependent protein kinase cascade. It has been associated with multiple processes including regulation of granulocyte function, activation of CREB-dependent gene transcription, aldosterone synthesis, differentiation and activation of neutrophil cells, and apoptosis of erythroleukemia cells. Alternatively spliced transcript variants encoding different isoforms of this gene have been described. [provided by RefSeq, Jan 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMK1D	NM_153498.4	c.93-95364G>A		intron_variant		ENST00000619168.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMK1D	ENST00000619168.5	c.93-95364G>A		intron_variant		1	NM_153498.4	P1
CAMK1D	ENST00000378845.5	c.93-95364G>A		intron_variant		1
CAMK1D	ENST00000487696.1	n.259+107951G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27272 AN: 151588 Hom.: 2677 Cov.: 31

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.0936

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.180 AC: 27330 AN: 151700 Hom.: 2689 Cov.: 31 AF XY: 0.180 AC XY: 13317 AN XY: 74132

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.0936

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.191

Alfa AF: 0.164 Hom.: 4572

Bravo AF: 0.182

Asia WGS AF: 0.246 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.55

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: rs2399849; hg19: chr10-12499860;