rs1067321

Variant names:

• chr2-44404173-G-T
• rs1067321
• NM_024766.5:c.376+13868G>T

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+13868G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,022 control chromosomes in the GnomAD database, including 41,597 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 0.73 (41597 hom., cov: 32)
• Consequence: CAMKMT NM_024766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.24
• Publications: 2 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]

LOC124907759 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMKMT	NM_024766.5	c.376+13868G>T		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+13868G>T		intron_variant	Intron 3 of 10	1	NM_024766.5	ENSP00000367755.3

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111284 AN: 151904 Hom.: 41559 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.733 AC: 111371 AN: 152022 Hom.: 41597 Cov.: 32 AF XY: 0.724 AC XY: 53743 AN XY: 74278

African (AFR) AF: 0.829 AC: 34417 AN: 41504

American (AMR) AF: 0.655 AC: 10003 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2629 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1698 AN: 5168

South Asian (SAS) AF: 0.790 AC: 3808 AN: 4822

European-Finnish (FIN) AF: 0.635 AC: 6701 AN: 10546

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49662 AN: 67934

Other (OTH) AF: 0.739 AC: 1556 AN: 2106

Alfa AF: 0.741 Hom.: 10270

Bravo AF: 0.733

Asia WGS AF: 0.616 AC: 2136 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	14
DANN	Benign	0.84
PhyloP100		2.2
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: rs1067321; hg19: chr2-44631312;