rs723211

Positions:

• chr10-12720304-G-A
• chr10-12720304-G-C

Variant summary

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

The NM_153498.4(CAMK1D):​c.300-40644G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,996 control chromosomes in the GnomAD database, including 20,550 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 0.52 (20550 hom., cov: 32)
• Consequence: CAMK1D NM_153498.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK1D	NM_153498.4	c.300-40644G>A		intron_variant		ENST00000619168.5	NP_705718.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK1D	ENST00000619168.5	c.300-40644G>A		intron_variant		1	NM_153498.4	ENSP00000478874.1
CAMK1D	ENST00000378845.5	c.300-40644G>A		intron_variant		1		ENSP00000368122.1

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78424 AN: 151878 Hom.: 20527 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.516 AC: 78502 AN: 151996 Hom.: 20550 Cov.: 32 AF XY: 0.515 AC XY: 38234 AN XY: 74304

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.556

Alfa AF: 0.504 Hom.: 18111

Bravo AF: 0.534

Asia WGS AF: 0.538 AC: 1866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.094
DANN	Benign	0.65

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: rs723211; hg19: chr10-12762303;