2-44401390-C-G

Variant names:

• chr2-44401390-C-G
• rs1067327
• NM_024766.5:c.376+11085C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024766.5(CAMKMT):​c.376+11085C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,654 control chromosomes in the GnomAD database, including 25,734 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 0.57 (25734 hom., cov: 29)
• Consequence: CAMKMT NM_024766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 7 publications found

Genes affected

CAMKMT (HGNC:26276): (calmodulin-lysine N-methyltransferase) This gene encodes a class I protein methyltransferase that acts in the formation of trimethyllysine in calmodulin. The protein contains a AdoMet-binding motif and may play a role in calcium-dependent signaling. [provided by RefSeq, Sep 2012]

LOC124907759 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMKMT	NM_024766.5	c.376+11085C>G		intron_variant	Intron 3 of 10	ENST00000378494.8	NP_079042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMKMT	ENST00000378494.8	c.376+11085C>G		intron_variant	Intron 3 of 10	1	NM_024766.5	ENSP00000367755.3

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86406 AN: 151536 Hom.: 25736 Cov.: 29

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.683

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.570 AC: 86422 AN: 151654 Hom.: 25734 Cov.: 29 AF XY: 0.565 AC XY: 41865 AN XY: 74120

African (AFR) AF: 0.417 AC: 17230 AN: 41322

American (AMR) AF: 0.568 AC: 8661 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2351 AN: 3468

East Asian (EAS) AF: 0.311 AC: 1593 AN: 5130

South Asian (SAS) AF: 0.661 AC: 3180 AN: 4812

European-Finnish (FIN) AF: 0.580 AC: 6090 AN: 10498

Middle Eastern (MID) AF: 0.679 AC: 197 AN: 290

European-Non Finnish (NFE) AF: 0.666 AC: 45232 AN: 67878

Other (OTH) AF: 0.586 AC: 1232 AN: 2102

Alfa AF: 0.609 Hom.: 3428

Bravo AF: 0.558

Asia WGS AF: 0.487 AC: 1699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.55
DANN	Benign	0.87
PhyloP100		-1.3
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: rs1067327; hg19: chr2-44628529;