2-44485790-A-G

Variant names:

• chr2-44485790-A-G
• rs698819
• NM_024766.5:c.376+95485A>G

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+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
• 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]

LOC124907758 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CAMKMT	NM_024766.5	c.376+95485A>G		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+95485A>G		intron_variant	Intron 3 of 10	1	NM_024766.5	ENSP00000367755.3
CAMKMT	ENST00000402247.5	c.377-63765A>G		intron_variant	Intron 3 of 3	2		ENSP00000385587.1
CAMKMT	ENST00000407131.5	c.376+95485A>G		intron_variant	Intron 3 of 3	3		ENSP00000384039.1
CAMKMT	ENST00000428993.1	n.206-63765A>G		intron_variant	Intron 2 of 3	3		ENSP00000410783.1

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

African (AFR) AF: 0.0318 AC: 1321 AN: 41556

American (AMR) AF: 0.175 AC: 2679 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3468

East Asian (EAS) AF: 0.239 AC: 1236 AN: 5174

South Asian (SAS) AF: 0.0837 AC: 404 AN: 4828

European-Finnish (FIN) AF: 0.110 AC: 1169 AN: 10602

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0769 AC: 5228 AN: 68022

Other (OTH) AF: 0.0962 AC: 203 AN: 2110

Alfa AF: 0.0826 Hom.: 2068

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
PhyloP100		0.12
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: rs698819; hg19: chr2-44712929;