rs17151584

chr10-12361029-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_153498.4(CAMK1D):c.92+11119A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0844 in 152,226 control chromosomes in the GnomAD database, including 716 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 0.084 (716 hom., cov: 32)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMK1D	NM_153498.4	c.92+11119A>G		intron_variant		ENST00000619168.5
CAMK1D	NM_020397.4	c.92+11119A>G		intron_variant
CAMK1D	XM_006717482.4	c.92+11119A>G		intron_variant
CAMK1D	XM_006717483.5	c.92+11119A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMK1D	ENST00000619168.5	c.92+11119A>G		intron_variant		1	NM_153498.4	P1
CAMK1D	ENST00000378845.5	c.92+11119A>G		intron_variant		1
CAMK1D	ENST00000487696.1	n.259+11119A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0845 AC: 12849 AN: 152108 Hom.: 716 Cov.: 32

Gnomad AFR AF: 0.0360

Gnomad AMI AF: 0.0582

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.0855

Gnomad FIN AF: 0.0803

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0878

Gnomad OTH AF: 0.0760

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

GnomAD4 genome AF: 0.0844 AC: 12849 AN: 152226 Hom.: 716 Cov.: 32 AF XY: 0.0873 AC XY: 6501 AN XY: 74438

Gnomad4 AFR AF: 0.0359

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.0854

Gnomad4 FIN AF: 0.0803

Gnomad4 NFE AF: 0.0878

Gnomad4 OTH AF: 0.0752

Alfa AF: 0.0903 Hom.: 946

Bravo AF: 0.0884

Asia WGS AF: 0.140 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.65
Dann	Benign	0.30

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

Publications

LitVar

Other links and lift over

dbSNP: rs17151584; hg19: chr10-12403028;