chr2-44434078-G-C

Variant names:

• chr2-44434078-G-C
• rs1067361
• NM_024766.5:c.376+43773G>C

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+43773G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,138 control chromosomes in the GnomAD database, including 43,242 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 (43242 hom., cov: 32)
• Consequence: CAMKMT NM_024766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 2 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAMKMT	NM_024766.5	c.376+43773G>C		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+43773G>C		intron_variant	Intron 3 of 10	1	NM_024766.5	ENSP00000367755.3

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113213 AN: 152020 Hom.: 43188 Cov.: 32

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.745 AC: 113322 AN: 152138 Hom.: 43242 Cov.: 32 AF XY: 0.735 AC XY: 54686 AN XY: 74380

African (AFR) AF: 0.874 AC: 36283 AN: 41530

American (AMR) AF: 0.665 AC: 10160 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.758 AC: 2631 AN: 3472

East Asian (EAS) AF: 0.321 AC: 1665 AN: 5180

South Asian (SAS) AF: 0.792 AC: 3814 AN: 4818

European-Finnish (FIN) AF: 0.633 AC: 6682 AN: 10556

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49597 AN: 67980

Other (OTH) AF: 0.750 AC: 1585 AN: 2112

Alfa AF: 0.741 Hom.: 5219

Bravo AF: 0.747

Asia WGS AF: 0.623 AC: 2169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.58
PhyloP100		-0.044
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: rs1067361; hg19: chr2-44661217;