rs1065783

Variant names:

• chr2-44433602-T-A
• rs1065783
• NM_024766.5:c.376+43297T>A

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+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
• Publications: 1 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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CAMKMT	NM_024766.5	c.376+43297T>A		intron_variant	Intron 3 of 10	ENST00000378494.8	NP_079042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAMKMT	ENST00000378494.8	c.376+43297T>A		intron_variant	Intron 3 of 10	1	NM_024766.5	ENSP00000367755.3

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

African (AFR) AF: 0.769 AC: 31876 AN: 41456

American (AMR) AF: 0.716 AC: 10906 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2678 AN: 3468

East Asian (EAS) AF: 0.667 AC: 3442 AN: 5160

South Asian (SAS) AF: 0.870 AC: 4196 AN: 4824

European-Finnish (FIN) AF: 0.680 AC: 7158 AN: 10528

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50313 AN: 67962

Other (OTH) AF: 0.760 AC: 1607 AN: 2114

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
PhyloP100		-0.14
Mutation Taster		=100/0	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: rs1065783; hg19: chr2-44660741;