10-12469763-A-G

Variant names:

• chr10-12469763-A-G
• rs2768412
• NM_153498.4:c.93-83462A>G

Variant summary

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

The NM_153498.4(CAMK1D):​c.93-83462A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,160 control chromosomes in the GnomAD database, including 11,181 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 0.38 (11181 hom., cov: 33)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 3 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMK1D	NM_153498.4	c.93-83462A>G		intron_variant	Intron 1 of 10	ENST00000619168.5	NP_705718.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMK1D	ENST00000619168.5	c.93-83462A>G		intron_variant	Intron 1 of 10	1	NM_153498.4	ENSP00000478874.1
CAMK1D	ENST00000378845.5	c.93-83462A>G		intron_variant	Intron 1 of 9	1		ENSP00000368122.1
CAMK1D	ENST00000487696.1	n.259+119853A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57691 AN: 152044 Hom.: 11182 Cov.: 33

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.379 AC: 57717 AN: 152160 Hom.: 11181 Cov.: 33 AF XY: 0.378 AC XY: 28128 AN XY: 74402

African (AFR) AF: 0.347 AC: 14393 AN: 41514

American (AMR) AF: 0.347 AC: 5297 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1216 AN: 3468

East Asian (EAS) AF: 0.276 AC: 1430 AN: 5188

South Asian (SAS) AF: 0.342 AC: 1648 AN: 4816

European-Finnish (FIN) AF: 0.454 AC: 4804 AN: 10582

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.406 AC: 27637 AN: 68004

Other (OTH) AF: 0.365 AC: 771 AN: 2112

Alfa AF: 0.395 Hom.: 5867

Bravo AF: 0.371

Asia WGS AF: 0.315 AC: 1095 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.4
DANN	Benign	0.68
PhyloP100		0.090
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: rs2768412; hg19: chr10-12511762;