2-44478476-A-G

Variant names:

• chr2-44478476-A-G
• rs698813
• NM_024766.5:c.376+88171A>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+88171A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 151,872 control chromosomes in the GnomAD database, including 49,811 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 0.81 (49811 hom., cov: 31)
• Consequence: CAMKMT NM_024766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 9 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]

LOC124907758 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024766.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMKMT	NM_024766.5	MANE Select	c.376+88171A>G		intron	N/A	NP_079042.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CAMKMT	ENST00000378494.8	TSL:1 MANE Select	c.376+88171A>G		intron	N/A	ENSP00000367755.3
	CAMKMT	ENST00000402247.5	TSL:2	c.377-71079A>G		intron	N/A	ENSP00000385587.1
	CAMKMT	ENST00000407131.5	TSL:3	c.376+88171A>G		intron	N/A	ENSP00000384039.1

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122345 AN: 151754 Hom.: 49745 Cov.: 31

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.806 AC: 122472 AN: 151872 Hom.: 49811 Cov.: 31 AF XY: 0.802 AC XY: 59538 AN XY: 74196

African (AFR) AF: 0.905 AC: 37552 AN: 41488

American (AMR) AF: 0.839 AC: 12808 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2814 AN: 3468

East Asian (EAS) AF: 0.692 AC: 3576 AN: 5168

South Asian (SAS) AF: 0.881 AC: 4236 AN: 4810

European-Finnish (FIN) AF: 0.699 AC: 7332 AN: 10486

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51501 AN: 67862

Other (OTH) AF: 0.815 AC: 1722 AN: 2112

Alfa AF: 0.783 Hom.: 57461

Bravo AF: 0.821

Asia WGS AF: 0.789 AC: 2741 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	13
DANN	Benign	0.78
PhyloP100		0.025
Mutation Taster		=99/1	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: rs698813; hg19: chr2-44705615;