rs12402938

Positions:

• chr1-209606010-A-G

Variant summary

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

The NM_020439.3(CAMK1G):​c.436-310A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,200 control chromosomes in the GnomAD database, including 2,857 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 0.19 (2857 hom., cov: 32)
• Consequence: CAMK1G NM_020439.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

Genes affected

CAMK1G (HGNC:14585): (calcium/calmodulin dependent protein kinase IG) Predicted to enable calmodulin binding activity and calmodulin-dependent protein kinase activity. Predicted to be involved in peptidyl-serine phosphorylation. Predicted to be located in endomembrane system. Predicted to be part of calcium- and calmodulin-dependent protein kinase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMK1G	NM_020439.3	c.436-310A>G		intron_variant		ENST00000361322.3	NP_065172.1
CAMK1G	XM_017001866.3	c.436-310A>G		intron_variant			XP_016857355.1
CAMK1G	XM_017001867.2	c.-45-310A>G		intron_variant			XP_016857356.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMK1G	ENST00000361322.3	c.436-310A>G		intron_variant		1	NM_020439.3	ENSP00000354861.2
CAMK1G	ENST00000009105.5	c.436-310A>G		intron_variant		2		ENSP00000009105.1
CAMK1G	ENST00000651530.1	c.148-310A>G		intron_variant				ENSP00000498823.1
CAMK1G	ENST00000423146.5	c.436-310A>G		intron_variant		3		ENSP00000392173.1

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28341 AN: 152082 Hom.: 2847 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.186 AC: 28366 AN: 152200 Hom.: 2857 Cov.: 32 AF XY: 0.183 AC XY: 13621 AN XY: 74410

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.0663

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.186

Alfa AF: 0.165 Hom.: 4199

Bravo AF: 0.192

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.5
DANN	Benign	0.79

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: rs12402938; hg19: chr1-209779355; COSMIC: COSV50526206; COSMIC: COSV50526206;