rs75263140

chr10-12660570-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_153498.4(CAMK1D):c.225-6166A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0264 in 152,284 control chromosomes in the GnomAD database, including 75 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 0.026 (75 hom., cov: 32)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.73

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=-0.97).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0264 (4023/152284) while in subpopulation SAS AF= 0.0485 (234/4824). AF 95% confidence interval is 0.0434. There are 75 homozygotes in gnomad4. There are 2025 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High AC in GnomAd at 4020 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMK1D	NM_153498.4	c.225-6166A>G		intron_variant		ENST00000619168.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMK1D	ENST00000619168.5	c.225-6166A>G		intron_variant		1	NM_153498.4	P1
CAMK1D	ENST00000378845.5	c.225-6166A>G		intron_variant		1
CAMK1D	ENST00000487696.1	n.260-6166A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0264 AC: 4020 AN: 152166 Hom.: 76 Cov.: 32

Gnomad AFR AF: 0.00719

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0190

Gnomad ASJ AF: 0.0204

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0481

Gnomad FIN AF: 0.0522

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0366

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0264 AC: 4023 AN: 152284 Hom.: 75 Cov.: 32 AF XY: 0.0272 AC XY: 2025 AN XY: 74452

Gnomad4 AFR AF: 0.00717

Gnomad4 AMR AF: 0.0189

Gnomad4 ASJ AF: 0.0204

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0485

Gnomad4 FIN AF: 0.0522

Gnomad4 NFE AF: 0.0366

Gnomad4 OTH AF: 0.0161

Alfa AF: 0.0365 Hom.: 25

Bravo AF: 0.0219

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.0040
Dann	Benign	0.40

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: rs75263140; hg19: chr10-12702569;