10-12702337-C-G

Position:

• chr10-12702337-C-G

Variant summary

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

The NM_153498.4(CAMK1D):​c.299+35527C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,146 control chromosomes in the GnomAD database, including 51,860 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 0.78 (51860 hom., cov: 31)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.890

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 (NFE) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK1D	NM_153498.4	c.299+35527C>G		intron_variant		ENST00000619168.5	NP_705718.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK1D	ENST00000619168.5	c.299+35527C>G		intron_variant		1	NM_153498.4	ENSP00000478874.1
CAMK1D	ENST00000378845.5	c.299+35527C>G		intron_variant		1		ENSP00000368122.1

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118599 AN: 152028 Hom.: 51864 Cov.: 31

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.991

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.780 AC: 118605 AN: 152146 Hom.: 51860 Cov.: 31 AF XY: 0.784 AC XY: 58327 AN XY: 74404

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.884

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.806

Gnomad4 FIN AF: 0.991

Gnomad4 NFE AF: 0.963

Gnomad4 OTH AF: 0.813

Alfa AF: 0.814 Hom.: 3267

Bravo AF: 0.756

Asia WGS AF: 0.838 AC: 2913 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.59
DANN	Benign	0.49

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: rs4623785; hg19: chr10-12744336;