10-12552695-T-C

Position:

• chr10-12552695-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.93-530T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.941 in 152,340 control chromosomes in the GnomAD database, including 67,696 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 0.94 (67696 hom., cov: 33)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.561

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]

CAMK1D (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 = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK1D	NM_153498.4	c.93-530T>C		intron_variant		ENST00000619168.5	NP_705718.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK1D	ENST00000619168.5	c.93-530T>C		intron_variant		1	NM_153498.4	ENSP00000478874.1
CAMK1D	ENST00000378845.5	c.93-530T>C		intron_variant		1		ENSP00000368122.1
CAMK1D	ENST00000487696.1	n.260-114041T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.941 AC: 143267 AN: 152222 Hom.: 67648 Cov.: 33

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.964

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.948

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

GnomAD4 genome AF: 0.941 AC: 143372 AN: 152340 Hom.: 67696 Cov.: 33 AF XY: 0.944 AC XY: 70300 AN XY: 74490

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.975

Gnomad4 ASJ AF: 0.964

Gnomad4 EAS AF: 0.992

Gnomad4 SAS AF: 0.978

Gnomad4 FIN AF: 0.987

Gnomad4 NFE AF: 0.974

Gnomad4 OTH AF: 0.949

Alfa AF: 0.969 Hom.: 92461

Bravo AF: 0.936

Asia WGS AF: 0.964 AC: 3355 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	5.3
DANN	Benign	0.62

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: rs2999981; hg19: chr10-12594694;