Genetic Variant CALM3:c.-157T>A (chr19-46601278-T-A) – ACMG Classification: Benign (-18 pts)

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_001329921.1(CALM3):c.-106+102T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 544,608 control chromosomes in the GnomAD database, including 11,146 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2483 hom., cov: 32)

Exomes 𝑓: 0.20 ( 8663 hom. )

Consequence

CALM3
NM_001329921.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.301

Variant links:

Genes affected

CALM3 (HGNC:1449): (calmodulin 3) This gene encodes a member of a family of proteins that binds calcium and functions as a enzymatic co-factor. Activity of this protein is important in the regulation of the cell cycle and cytokinesis. Multiple alternatively spliced transcript variants have been observed at this gene. [provided by RefSeq, Aug 2016]

CALM3 links:

PPP5D1P (HGNC:):

PPP5D1P links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.29).

BP6

Variant 19-46601278-T-A is Benign according to our data. Variant chr19-46601278-T-A is described in ClinVar as [Benign]. Clinvar id is 1167461.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CALM3	NM_005184.4 link	c.-157T>A		upstream_gene_variant		ENST00000291295.14	NP_005175.2	P0DP23P0DP24P0DP25B4DJ51Q9BRL5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CALM3	ENST00000291295.14 link	c.-157T>A		upstream_gene_variant		1	NM_005184.4	ENSP00000291295.8		P0DP25

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

23885

AN:

148300

Hom.:

2484

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0709

Gnomad AMI

AF:

0.248

Gnomad AMR

AF:

0.123

Gnomad ASJ

AF:

0.0911

Gnomad EAS

AF:

0.379

Gnomad SAS

AF:

0.143

Gnomad FIN

AF:

0.308

Gnomad MID

AF:

0.0487

Gnomad NFE

AF:

0.192

Gnomad OTH

AF:

0.139

GnomAD4 exome

AF:

0.198

AC:

78428

AN:

396200

Hom.:

8663

Cov.:

AF XY:

0.199

AC XY:

39581

AN XY:

198484

show subpopulations

Gnomad4 AFR exome

AF:

0.0593

Gnomad4 AMR exome

AF:

0.117

Gnomad4 ASJ exome

AF:

0.0901

Gnomad4 EAS exome

AF:

0.329

Gnomad4 SAS exome

AF:

0.195

Gnomad4 FIN exome

AF:

0.331

Gnomad4 NFE exome

AF:

0.196

Gnomad4 OTH exome

AF:

0.191

GnomAD4 genome

AF:

0.161

AC:

23882

AN:

148408

Hom.:

2483

Cov.:

AF XY:

0.165

AC XY:

11974

AN XY:

72438

show subpopulations

Gnomad4 AFR

AF:

0.0708

Gnomad4 AMR

AF:

0.122

Gnomad4 ASJ

AF:

0.0911

Gnomad4 EAS

AF:

0.379

Gnomad4 SAS

AF:

0.143

Gnomad4 FIN

AF:

0.308

Gnomad4 NFE

AF:

0.192

Gnomad4 OTH

AF:

0.138

Alfa

AF:

0.163

Hom.:

282

Bravo

AF:

0.144

Asia WGS

AF:

0.245

AC:

825

AN:

3374

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 19, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 19429631) -

Long QT syndrome 1

Benign:1

Jan 20, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.29

CADD

Benign

DANN

Benign

0.93

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over