rs1067321

Positions:

• chr2-44404173-G-T

Variant summary

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

The NM_024766.5(CAMKMT):​c.376+13868G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,022 control chromosomes in the GnomAD database, including 41,597 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 0.73 (41597 hom., cov: 32)
• Consequence: CAMKMT NM_024766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.24

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]

LOC124907759 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAMKMT	NM_024766.5	c.376+13868G>T		intron_variant		ENST00000378494.8
LOC124907759	XR_007086304.1	n.74+2967G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAMKMT	ENST00000378494.8	c.376+13868G>T		intron_variant		1	NM_024766.5	P1

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111284 AN: 151904 Hom.: 41559 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.733 AC: 111371 AN: 152022 Hom.: 41597 Cov.: 32 AF XY: 0.724 AC XY: 53743 AN XY: 74278

Gnomad4 AFR AF: 0.829

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.757

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.739

Alfa AF: 0.741 Hom.: 9006

Bravo AF: 0.733

Asia WGS AF: 0.616 AC: 2136 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	14
DANN	Benign	0.84

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: rs1067321; hg19: chr2-44631312;