rs1892302

chr10-12404573-T-C

Variant summary

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

The NM_153498.4(CAMK1D):c.92+54663T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,064 control chromosomes in the GnomAD database, including 38,796 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 0.71 (38796 hom., cov: 32)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMK1D	NM_153498.4	c.92+54663T>C		intron_variant		ENST00000619168.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMK1D	ENST00000619168.5	c.92+54663T>C		intron_variant		1	NM_153498.4	P1
CAMK1D	ENST00000378845.5	c.92+54663T>C		intron_variant		1
CAMK1D	ENST00000487696.1	n.259+54663T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108296 AN: 151946 Hom.: 38758 Cov.: 32

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.713 AC: 108392 AN: 152064 Hom.: 38796 Cov.: 32 AF XY: 0.715 AC XY: 53133 AN XY: 74334

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.744

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.738

Alfa AF: 0.722 Hom.: 24576

Bravo AF: 0.714

Asia WGS AF: 0.673 AC: 2341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	4.4
Dann	Benign	0.56

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: rs1892302; hg19: chr10-12446572; COSMIC: COSV66616775;