10-12552695-T-C

Variant names:

• chr10-12552695-T-C
• rs2999981
• NM_153498.4:c.93-530T>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.93-530T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.941 in 152,340 control chromosomes in the GnomAD database, including 67,696 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 0.94 (67696 hom., cov: 33)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.561
• Publications: 2 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 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.93-530T>C		intron	N/A	NP_705718.1	Q8IU85-1
	CAMK1D	NM_020397.4		c.93-530T>C		intron	N/A	NP_065130.1	Q5SQQ7
	CAMK1D	NM_001351032.2		c.-199-530T>C		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.93-530T>C		intron	N/A	ENSP00000478874.1	Q8IU85-1
	CAMK1D	ENST00000378845.5	TSL:1	c.93-530T>C		intron	N/A	ENSP00000368122.1	Q8IU85-2
	CAMK1D	ENST00000487696.1	TSL:3	n.260-114041T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.941 AC: 143267 AN: 152222 Hom.: 67648 Cov.: 33

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.964

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.987

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.974

Gnomad OTH AF: 0.948

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

GnomAD4 genome AF: 0.941 AC: 143372 AN: 152340 Hom.: 67696 Cov.: 33 AF XY: 0.944 AC XY: 70300 AN XY: 74490

African (AFR) AF: 0.850 AC: 35311 AN: 41558

American (AMR) AF: 0.975 AC: 14920 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.964 AC: 3346 AN: 3472

East Asian (EAS) AF: 0.992 AC: 5148 AN: 5188

South Asian (SAS) AF: 0.978 AC: 4714 AN: 4822

European-Finnish (FIN) AF: 0.987 AC: 10482 AN: 10622

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.974 AC: 66258 AN: 68048

Other (OTH) AF: 0.949 AC: 2006 AN: 2114

Alfa AF: 0.966 Hom.: 116778

Bravo AF: 0.936

Asia WGS AF: 0.964 AC: 3355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.62
PhyloP100		0.56
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: rs2999981; hg19: chr10-12594694;