rs12402938

Variant names:

• chr1-209606010-A-G
• rs12402938
• NM_020439.3:c.436-310A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CAMK1G	NM_020439.3	c.436-310A>G		intron_variant	Intron 5 of 12	ENST00000361322.3	NP_065172.1
CAMK1G	XM_017001866.3	c.436-310A>G		intron_variant	Intron 5 of 12		XP_016857355.1
CAMK1G	XM_017001867.2	c.-45-310A>G		intron_variant	Intron 2 of 9		XP_016857356.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMK1G	ENST00000361322.3	c.436-310A>G		intron_variant	Intron 5 of 12	1	NM_020439.3	ENSP00000354861.2
CAMK1G	ENST00000009105.5	c.436-310A>G		intron_variant	Intron 5 of 12	2		ENSP00000009105.1
CAMK1G	ENST00000651530.1	c.148-310A>G		intron_variant	Intron 6 of 13			ENSP00000498823.1
CAMK1G	ENST00000423146.5	c.436-310A>G		intron_variant	Intron 5 of 7	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

African (AFR) AF: 0.249 AC: 10321 AN: 41500

American (AMR) AF: 0.190 AC: 2907 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3472

East Asian (EAS) AF: 0.132 AC: 684 AN: 5178

South Asian (SAS) AF: 0.0663 AC: 320 AN: 4828

European-Finnish (FIN) AF: 0.188 AC: 1989 AN: 10598

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11063 AN: 68006

Other (OTH) AF: 0.186 AC: 394 AN: 2114

Alfa AF: 0.169 Hom.: 9440

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
PhyloP100		0.018
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: rs12402938; hg19: chr1-209779355; COSMIC: COSV50526206; COSMIC: COSV50526206;