NM_153498.4:c.93-56733G>A

Variant names:

• chr10-12496492-G-A
• rs7078980
• NM_153498.4:c.93-56733G>A

Variant summary

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

The NM_153498.4(CAMK1D):​c.93-56733G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,966 control chromosomes in the GnomAD database, including 3,378 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 0.21 (3378 hom., cov: 31)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMK1D	NM_153498.4	c.93-56733G>A		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.93-56733G>A		intron_variant	Intron 1 of 10	1	NM_153498.4	ENSP00000478874.1
CAMK1D	ENST00000378845.5	c.93-56733G>A		intron_variant	Intron 1 of 9	1		ENSP00000368122.1
CAMK1D	ENST00000487696.1	n.259+146582G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31736 AN: 151848 Hom.: 3374 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.209 AC: 31754 AN: 151966 Hom.: 3378 Cov.: 31 AF XY: 0.208 AC XY: 15480 AN XY: 74282

African (AFR) AF: 0.214 AC: 8853 AN: 41402

American (AMR) AF: 0.189 AC: 2879 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 485 AN: 3472

East Asian (EAS) AF: 0.103 AC: 533 AN: 5164

South Asian (SAS) AF: 0.173 AC: 831 AN: 4808

European-Finnish (FIN) AF: 0.274 AC: 2893 AN: 10564

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.216 AC: 14699 AN: 67974

Other (OTH) AF: 0.184 AC: 388 AN: 2108

Alfa AF: 0.208 Hom.: 12262

Bravo AF: 0.203

Asia WGS AF: 0.138 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.5
DANN	Benign	0.74
PhyloP100		0.40
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: rs7078980; hg19: chr10-12538491;