chr10-12549713-C-T

Position:

• chr10-12549713-C-T

Variant summary

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

The NM_153498.4(CAMK1D):​c.93-3512C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,016 control chromosomes in the GnomAD database, including 25,100 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 0.57 (25100 hom., cov: 32)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK1D	NM_153498.4	c.93-3512C>T		intron_variant		ENST00000619168.5	NP_705718.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK1D	ENST00000619168.5	c.93-3512C>T		intron_variant		1	NM_153498.4	ENSP00000478874.1
CAMK1D	ENST00000378845.5	c.93-3512C>T		intron_variant		1		ENSP00000368122.1
CAMK1D	ENST00000487696.1	n.260-117023C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86837 AN: 151898 Hom.: 25098 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.571 AC: 86870 AN: 152016 Hom.: 25100 Cov.: 32 AF XY: 0.567 AC XY: 42158 AN XY: 74294

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.571

Alfa AF: 0.587 Hom.: 46727

Bravo AF: 0.561

Asia WGS AF: 0.417 AC: 1453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.65
DANN	Benign	0.33

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: rs7897059; hg19: chr10-12591712;