chr2-44433477-A-C

Position:

• chr2-44433477-A-C

Variant summary

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

The NM_024766.5(CAMKMT):​c.376+43172A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,882 control chromosomes in the GnomAD database, including 32,501 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 0.65 (32501 hom., cov: 31)
• Consequence: CAMKMT NM_024766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14

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]

CAMKMT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CAMKMT	NM_024766.5	c.376+43172A>C		intron_variant		ENST00000378494.8	NP_079042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CAMKMT	ENST00000378494.8	c.376+43172A>C		intron_variant		1	NM_024766.5	ENSP00000367755.3

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99229 AN: 151764 Hom.: 32501 Cov.: 31

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.654 AC: 99265 AN: 151882 Hom.: 32501 Cov.: 31 AF XY: 0.650 AC XY: 48288 AN XY: 74268

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.658

Alfa AF: 0.598 Hom.: 3271

Bravo AF: 0.652

Asia WGS AF: 0.644 AC: 2237 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.2
DANN	Benign	0.79
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1065786; hg19: chr2-44660616;