rs1892302

Variant names:

• chr10-12404573-T-C
• rs1892302
• NM_153498.4:c.92+54663T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000619168.5(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 ENST00000619168.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000619168.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMK1D	NM_153498.4	MANE Select	c.92+54663T>C		intron	N/A	NP_705718.1
	CAMK1D	NM_020397.4		c.92+54663T>C		intron	N/A	NP_065130.1
	CAMK1D	NM_001351032.2		c.-200+1204T>C		intron	N/A	NP_001337961.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMK1D	ENST00000619168.5	TSL:1 MANE Select	c.92+54663T>C		intron	N/A	ENSP00000478874.1
	CAMK1D	ENST00000378845.5	TSL:1	c.92+54663T>C		intron	N/A	ENSP00000368122.1
	CAMK1D	ENST00000487696.1	TSL:3	n.259+54663T>C		intron	N/A

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

African (AFR) AF: 0.670 AC: 27797 AN: 41484

American (AMR) AF: 0.755 AC: 11528 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2820 AN: 3472

East Asian (EAS) AF: 0.704 AC: 3638 AN: 5168

South Asian (SAS) AF: 0.733 AC: 3535 AN: 4822

European-Finnish (FIN) AF: 0.744 AC: 7860 AN: 10564

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48689 AN: 67968

Other (OTH) AF: 0.738 AC: 1558 AN: 2110

Alfa AF: 0.720 Hom.: 38646

Bravo AF: 0.714

Asia WGS AF: 0.673 AC: 2341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.4
DANN	Benign	0.56
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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