rs698819

chr2-44485790-A-G

Variant summary

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

The NM_024766.5(CAMKMT):c.376+95485A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0833 in 152,250 control chromosomes in the GnomAD database, including 711 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 0.083 (711 hom., cov: 33)
• Consequence: CAMKMT NM_024766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

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]

LOC124907758 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMKMT	NM_024766.5	c.376+95485A>G		intron_variant		ENST00000378494.8
LOC124907758	XR_007086302.1	n.10000A>G		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMKMT	ENST00000378494.8	c.376+95485A>G		intron_variant		1	NM_024766.5	P1
CAMKMT	ENST00000402247.5	c.377-63765A>G		intron_variant		2
CAMKMT	ENST00000407131.5	c.376+95485A>G		intron_variant		3
CAMKMT	ENST00000428993.1	c.207-63765A>G		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0832 AC: 12658 AN: 152132 Hom.: 701 Cov.: 33

Gnomad AFR AF: 0.0317

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.0832

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0769

Gnomad OTH AF: 0.0934

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

GnomAD4 genome AF: 0.0833 AC: 12685 AN: 152250 Hom.: 711 Cov.: 33 AF XY: 0.0876 AC XY: 6520 AN XY: 74434

Gnomad4 AFR AF: 0.0318

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.0837

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.0769

Gnomad4 OTH AF: 0.0962

Alfa AF: 0.0831 Hom.: 1272

Bravo AF: 0.0894

Asia WGS AF: 0.164 AC: 569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.0
Dann	Benign	0.52

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: rs698819; hg19: chr2-44712929;