rs698798

Variant names:

• chr2-44463375-A-C
• rs698798
• NM_024766.5:c.376+73070A>C

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+73070A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,284 control chromosomes in the GnomAD database, including 1,234 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 0.12 (1234 hom., cov: 33)
• Consequence: CAMKMT NM_024766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447
• Publications: 4 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]

LOC124905999 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMKMT	NM_024766.5	c.376+73070A>C		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+73070A>C		intron_variant	Intron 3 of 10	1	NM_024766.5	ENSP00000367755.3
CAMKMT	ENST00000402247.5	c.376+73070A>C		intron_variant	Intron 3 of 3	2		ENSP00000385587.1
CAMKMT	ENST00000407131.5	c.376+73070A>C		intron_variant	Intron 3 of 3	3		ENSP00000384039.1
CAMKMT	ENST00000428993.1	n.205+73070A>C		intron_variant	Intron 2 of 3	3		ENSP00000410783.1

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17701 AN: 152166 Hom.: 1221 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.0958

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.0580

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0801

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.117 AC: 17743 AN: 152284 Hom.: 1234 Cov.: 33 AF XY: 0.115 AC XY: 8557 AN XY: 74480

African (AFR) AF: 0.178 AC: 7391 AN: 41544

American (AMR) AF: 0.185 AC: 2836 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0677 AC: 235 AN: 3470

East Asian (EAS) AF: 0.0950 AC: 493 AN: 5188

South Asian (SAS) AF: 0.0775 AC: 374 AN: 4828

European-Finnish (FIN) AF: 0.0580 AC: 616 AN: 10614

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0801 AC: 5450 AN: 68024

Other (OTH) AF: 0.119 AC: 251 AN: 2114

Alfa AF: 0.0964 Hom.: 1503

Bravo AF: 0.132

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.9
DANN	Benign	0.76
PhyloP100		0.45
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: rs698798; hg19: chr2-44690514;