rs1065783

Positions:

• chr2-44433602-T-A

Variant summary

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

The NM_024766.5(CAMKMT):​c.376+43297T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 151,958 control chromosomes in the GnomAD database, including 42,205 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 0.74 (42205 hom., cov: 31)
• Consequence: CAMKMT NM_024766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMKMT	NM_024766.5	c.376+43297T>A		intron_variant		ENST00000378494.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMKMT	ENST00000378494.8	c.376+43297T>A		intron_variant		1	NM_024766.5	P1

Frequencies

GnomAD3 genomes AF: 0.744 AC: 113034 AN: 151840 Hom.: 42184 Cov.: 31

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.760

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

GnomAD4 genome AF: 0.744 AC: 113101 AN: 151958 Hom.: 42205 Cov.: 31 AF XY: 0.741 AC XY: 54986 AN XY: 74226

Gnomad4 AFR AF: 0.769

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.772

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.760

Alfa AF: 0.737 Hom.: 5134

Bravo AF: 0.745

Asia WGS AF: 0.760 AC: 2623 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.42

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: rs1065783; hg19: chr2-44660741;