chr2-44433602-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024766.5(CAMKMT):​c.376+43297T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 151,958 control chromosomes in the GnomAD database, including 42,205 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 0.74 ( 42205 hom., cov: 31)

Consequence

CAMKMT
NM_024766.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.140
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CAMKMTNM_024766.5 linkuse as main transcriptc.376+43297T>A intron_variant ENST00000378494.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CAMKMTENST00000378494.8 linkuse as main transcriptc.376+43297T>A intron_variant 1 NM_024766.5 P1Q7Z624-1

Frequencies

GnomAD3 genomes
AF:
0.744
AC:
113034
AN:
151840
Hom.:
42184
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.769
Gnomad AMI
AF:
0.741
Gnomad AMR
AF:
0.716
Gnomad ASJ
AF:
0.772
Gnomad EAS
AF:
0.667
Gnomad SAS
AF:
0.869
Gnomad FIN
AF:
0.680
Gnomad MID
AF:
0.842
Gnomad NFE
AF:
0.740
Gnomad OTH
AF:
0.760
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.744
AC:
113101
AN:
151958
Hom.:
42205
Cov.:
31
AF XY:
0.741
AC XY:
54986
AN XY:
74226
show subpopulations
Gnomad4 AFR
AF:
0.769
Gnomad4 AMR
AF:
0.716
Gnomad4 ASJ
AF:
0.772
Gnomad4 EAS
AF:
0.667
Gnomad4 SAS
AF:
0.870
Gnomad4 FIN
AF:
0.680
Gnomad4 NFE
AF:
0.740
Gnomad4 OTH
AF:
0.760
Alfa
AF:
0.737
Hom.:
5134
Bravo
AF:
0.745
Asia WGS
AF:
0.760
AC:
2623
AN:
3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
2.0
DANN
Benign
0.42

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1065783; hg19: chr2-44660741; API