rs17498753

chr2-44420692-A-Gchr2-44420692-A-T

Variant summary

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

The NM_024766.5(CAMKMT):c.376+30387A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,106 control chromosomes in the GnomAD database, including 1,670 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 0.13 (1670 hom., cov: 32)
• Consequence: CAMKMT NM_024766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.401

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 (SAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMKMT	NM_024766.5	c.376+30387A>G		intron_variant		ENST00000378494.8
LOC124907759	XR_007086304.1	n.8754A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMKMT	ENST00000378494.8	c.376+30387A>G		intron_variant		1	NM_024766.5	P1

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19322 AN: 151988 Hom.: 1668 Cov.: 32

Gnomad AFR AF: 0.0314

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0396

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.127 AC: 19331 AN: 152106 Hom.: 1670 Cov.: 32 AF XY: 0.130 AC XY: 9697 AN XY: 74380

Gnomad4 AFR AF: 0.0314

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.0399

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.139

Alfa AF: 0.145 Hom.: 1147

Bravo AF: 0.127

Asia WGS AF: 0.121 AC: 420 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.6
Dann	Benign	0.67

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: rs17498753; hg19: chr2-44647831;