chr10-12549713-C-T

Variant names:

• chr10-12549713-C-T
• rs7897059
• NM_153498.4:c.93-3512C>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.93-3512C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,016 control chromosomes in the GnomAD database, including 25,100 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 0.57 (25100 hom., cov: 32)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 6 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.601 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.93-3512C>T		intron	N/A	NP_705718.1	Q8IU85-1
	CAMK1D	NM_020397.4		c.93-3512C>T		intron	N/A	NP_065130.1	Q5SQQ7
	CAMK1D	NM_001351032.2		c.-199-3512C>T		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.93-3512C>T		intron	N/A	ENSP00000478874.1	Q8IU85-1
	CAMK1D	ENST00000378845.5	TSL:1	c.93-3512C>T		intron	N/A	ENSP00000368122.1	Q8IU85-2
	CAMK1D	ENST00000487696.1	TSL:3	n.260-117023C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86837 AN: 151898 Hom.: 25098 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.571 AC: 86870 AN: 152016 Hom.: 25100 Cov.: 32 AF XY: 0.567 AC XY: 42158 AN XY: 74294

African (AFR) AF: 0.578 AC: 23942 AN: 41426

American (AMR) AF: 0.450 AC: 6870 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1952 AN: 3470

East Asian (EAS) AF: 0.463 AC: 2397 AN: 5172

South Asian (SAS) AF: 0.488 AC: 2354 AN: 4824

European-Finnish (FIN) AF: 0.588 AC: 6212 AN: 10560

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41197 AN: 67984

Other (OTH) AF: 0.571 AC: 1203 AN: 2106

Alfa AF: 0.587 Hom.: 102378

Bravo AF: 0.561

Asia WGS AF: 0.417 AC: 1453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.65
DANN	Benign	0.33
PhyloP100		-1.4
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: rs7897059; hg19: chr10-12591712;