rs75263140

Variant names:

• chr10-12660570-A-G
• rs75263140
• NM_153498.4:c.225-6166A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_153498.4(CAMK1D):​c.225-6166A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0264 in 152,284 control chromosomes in the GnomAD database, including 75 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 0.026 (75 hom., cov: 32)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73
• Publications: 7 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=-0.97).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0264 (4023/152284) while in subpopulation SAS AF = 0.0485 (234/4824). AF 95% confidence interval is 0.0434. There are 75 homozygotes in GnomAd4. There are 2025 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High AC in GnomAd4 at 4023 AD gene.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMK1D	NM_153498.4	MANE Select	c.225-6166A>G		intron	N/A	NP_705718.1
	CAMK1D	NM_020397.4		c.225-6166A>G		intron	N/A	NP_065130.1
	CAMK1D	NM_001351032.2		c.-67-6166A>G		intron	N/A	NP_001337961.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMK1D	ENST00000619168.5	TSL:1 MANE Select	c.225-6166A>G		intron	N/A	ENSP00000478874.1
	CAMK1D	ENST00000378845.5	TSL:1	c.225-6166A>G		intron	N/A	ENSP00000368122.1
	CAMK1D	ENST00000487696.1	TSL:3	n.260-6166A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0264 AC: 4020 AN: 152166 Hom.: 76 Cov.: 32

Gnomad AFR AF: 0.00719

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0190

Gnomad ASJ AF: 0.0204

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0481

Gnomad FIN AF: 0.0522

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0366

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0264 AC: 4023 AN: 152284 Hom.: 75 Cov.: 32 AF XY: 0.0272 AC XY: 2025 AN XY: 74452

African (AFR) AF: 0.00717 AC: 298 AN: 41552

American (AMR) AF: 0.0189 AC: 290 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0204 AC: 71 AN: 3472

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5188

South Asian (SAS) AF: 0.0485 AC: 234 AN: 4824

European-Finnish (FIN) AF: 0.0522 AC: 553 AN: 10600

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0366 AC: 2490 AN: 68024

Other (OTH) AF: 0.0161 AC: 34 AN: 2114

Alfa AF: 0.0317 Hom.: 153

Bravo AF: 0.0219

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0040
DANN	Benign	0.40
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism

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: rs75263140; hg19: chr10-12702569;