rs2341459

Positions:

• chr2-44541063-T-C

Variant summary

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

The NM_024766.5(CAMKMT):​c.376+150758T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 152,010 control chromosomes in the GnomAD database, including 37,999 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 0.70 (37999 hom., cov: 32)
• Consequence: CAMKMT NM_024766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMKMT	NM_024766.5	c.376+150758T>C		intron_variant		ENST00000378494.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMKMT	ENST00000378494.8	c.376+150758T>C		intron_variant		1	NM_024766.5	P1
CAMKMT	ENST00000402247.5	c.377-8492T>C		intron_variant		2
CAMKMT	ENST00000407131.5	c.377-90428T>C		intron_variant		3
CAMKMT	ENST00000428993.1	c.207-8492T>C		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106582 AN: 151892 Hom.: 37950 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.702 AC: 106690 AN: 152010 Hom.: 37999 Cov.: 32 AF XY: 0.698 AC XY: 51856 AN XY: 74306

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.771

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.734

Gnomad4 OTH AF: 0.742

Alfa AF: 0.729 Hom.: 87725

Bravo AF: 0.705

Asia WGS AF: 0.601 AC: 2088 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.69

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: rs2341459; hg19: chr2-44768202;