2-44463375-A-C

Position:

• chr2-44463375-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+73070A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,284 control chromosomes in the GnomAD database, including 1,234 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 0.12 (1234 hom., cov: 33)
• Consequence: CAMKMT NM_024766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMKMT	NM_024766.5	c.376+73070A>C		intron_variant		ENST00000378494.8
LOC124905999	XR_007086303.1	n.20056A>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMKMT	ENST00000378494.8	c.376+73070A>C		intron_variant		1	NM_024766.5	P1
CAMKMT	ENST00000402247.5	c.376+73070A>C		intron_variant		2
CAMKMT	ENST00000407131.5	c.376+73070A>C		intron_variant		3
CAMKMT	ENST00000428993.1	c.206+73070A>C		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17701 AN: 152166 Hom.: 1221 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.0677

Gnomad EAS AF: 0.0958

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.0580

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0801

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.117 AC: 17743 AN: 152284 Hom.: 1234 Cov.: 33 AF XY: 0.115 AC XY: 8557 AN XY: 74480

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.0677

Gnomad4 EAS AF: 0.0950

Gnomad4 SAS AF: 0.0775

Gnomad4 FIN AF: 0.0580

Gnomad4 NFE AF: 0.0801

Gnomad4 OTH AF: 0.119

Alfa AF: 0.0912 Hom.: 1052

Bravo AF: 0.132

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.9
DANN	Benign	0.76

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: rs698798; hg19: chr2-44690514;