2-44401390-C-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CAMKMT	NM_024766.5	c.376+11085C>G		intron_variant		ENST00000378494.8
LOC124907759	XR_007086304.1	n.74+184C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMKMT	ENST00000378494.8	c.376+11085C>G		intron_variant		1	NM_024766.5	P1

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

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.586

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

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: rs1067327; hg19: chr2-44628529;