chr10-12393380-C-T

Position:

• chr10-12393380-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.92+43470C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,954 control chromosomes in the GnomAD database, including 3,559 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 0.20 (3559 hom., cov: 32)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK1D	NM_153498.4	c.92+43470C>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.92+43470C>T		intron_variant		1	NM_153498.4	ENSP00000478874	P1
CAMK1D	ENST00000378845.5	c.92+43470C>T		intron_variant		1		ENSP00000368122
CAMK1D	ENST00000487696.1	n.259+43470C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30053 AN: 151836 Hom.: 3559 Cov.: 32

Gnomad AFR AF: 0.0644

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.198 AC: 30055 AN: 151954 Hom.: 3559 Cov.: 32 AF XY: 0.198 AC XY: 14700 AN XY: 74242

Gnomad4 AFR AF: 0.0643

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.223

Alfa AF: 0.251 Hom.: 6592

Bravo AF: 0.201

Asia WGS AF: 0.208 AC: 724 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	6.1
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: rs4750211; hg19: chr10-12435379;