rs10495918

chr2-44444219-G-A

Variant summary

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

The NM_024766.5(CAMKMT):c.376+53914G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0459 in 152,236 control chromosomes in the GnomAD database, including 407 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 0.046 (407 hom., cov: 32)
• Consequence: CAMKMT NM_024766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMKMT	NM_024766.5	c.376+53914G>A		intron_variant		ENST00000378494.8
LOC124905999	XR_007086303.1	n.900G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMKMT	ENST00000378494.8	c.376+53914G>A		intron_variant		1	NM_024766.5	P1

Frequencies

GnomAD3 genomes AF: 0.0460 AC: 6992 AN: 152118 Hom.: 410 Cov.: 32

Gnomad AFR AF: 0.0630

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0647

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.0800

Gnomad FIN AF: 0.0487

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0112

Gnomad OTH AF: 0.0393

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

GnomAD4 genome AF: 0.0459 AC: 6985 AN: 152236 Hom.: 407 Cov.: 32 AF XY: 0.0494 AC XY: 3674 AN XY: 74418

Gnomad4 AFR AF: 0.0629

Gnomad4 AMR AF: 0.0644

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.0794

Gnomad4 FIN AF: 0.0487

Gnomad4 NFE AF: 0.0112

Gnomad4 OTH AF: 0.0384

Alfa AF: 0.0253 Hom.: 33

Bravo AF: 0.0501

Asia WGS AF: 0.141 AC: 488 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.5
Dann	Benign	0.72

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: rs10495918; hg19: chr2-44671358;