10-12548176-C-T

Variant names:

• chr10-12548176-C-T
• rs4747989
• NM_153498.4:c.93-5049C>T

Variant summary

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

The NM_153498.4(CAMK1D):​c.93-5049C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,086 control chromosomes in the GnomAD database, including 2,187 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 0.15 (2187 hom., cov: 31)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMK1D	NM_153498.4	c.93-5049C>T		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.93-5049C>T		intron_variant	Intron 1 of 10	1	NM_153498.4	ENSP00000478874.1
CAMK1D	ENST00000378845.5	c.93-5049C>T		intron_variant	Intron 1 of 9	1		ENSP00000368122.1
CAMK1D	ENST00000487696.1	n.260-118560C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22038 AN: 151968 Hom.: 2179 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0738

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.145 AC: 22080 AN: 152086 Hom.: 2187 Cov.: 31 AF XY: 0.153 AC XY: 11341 AN XY: 74356

African (AFR) AF: 0.215 AC: 8935 AN: 41468

American (AMR) AF: 0.250 AC: 3816 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0597 AC: 207 AN: 3468

East Asian (EAS) AF: 0.299 AC: 1544 AN: 5156

South Asian (SAS) AF: 0.189 AC: 911 AN: 4822

European-Finnish (FIN) AF: 0.127 AC: 1345 AN: 10578

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0738 AC: 5022 AN: 68006

Other (OTH) AF: 0.128 AC: 271 AN: 2114

Alfa AF: 0.101 Hom.: 3544

Bravo AF: 0.155

Asia WGS AF: 0.263 AC: 912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.0
DANN	Benign	0.61
PhyloP100		1.1
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: rs4747989; hg19: chr10-12590175;