rs10906142

Variant names:

• chr10-12396784-G-A
• rs10906142
• NM_153498.4:c.92+46874G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-12396784-G-A
• chr10-12396784-G-C

Variant summary

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

The NM_153498.4(CAMK1D):​c.92+46874G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,010 control chromosomes in the GnomAD database, including 7,068 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 0.29 (7068 hom., cov: 32)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311
• Publications: 16 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153498.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMK1D	NM_153498.4	MANE Select	c.92+46874G>A		intron	N/A	NP_705718.1	Q8IU85-1
	CAMK1D	NM_020397.4		c.92+46874G>A		intron	N/A	NP_065130.1	Q5SQQ7
	CAMK1D	NM_001351032.2		c.-467-6318G>A		intron	N/A	NP_001337961.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMK1D	ENST00000619168.5	TSL:1 MANE Select	c.92+46874G>A		intron	N/A	ENSP00000478874.1	Q8IU85-1
	CAMK1D	ENST00000378845.5	TSL:1	c.92+46874G>A		intron	N/A	ENSP00000368122.1	Q8IU85-2
	CAMK1D	ENST00000487696.1	TSL:3	n.259+46874G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44801 AN: 151892 Hom.: 7061 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.295 AC: 44808 AN: 152010 Hom.: 7068 Cov.: 32 AF XY: 0.299 AC XY: 22244 AN XY: 74282

African (AFR) AF: 0.208 AC: 8648 AN: 41478

American (AMR) AF: 0.269 AC: 4116 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 806 AN: 3466

East Asian (EAS) AF: 0.544 AC: 2805 AN: 5154

South Asian (SAS) AF: 0.323 AC: 1555 AN: 4812

European-Finnish (FIN) AF: 0.372 AC: 3920 AN: 10542

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.325 AC: 22055 AN: 67964

Other (OTH) AF: 0.290 AC: 613 AN: 2112

Alfa AF: 0.304 Hom.: 14362

Bravo AF: 0.283

Asia WGS AF: 0.434 AC: 1508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.57
PhyloP100		-0.31
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: rs10906142; hg19: chr10-12438783;