Genetic Variant NM_001363669.2:c.-106+355C>T (chr14-90397013-C-T) – 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_001363669.2(CALM1):c.-106+355C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 586,668 control chromosomes in the GnomAD database, including 72,424 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 14991 hom., cov: 33)

Exomes 𝑓: 0.50 ( 57433 hom. )

Consequence

CALM1
NM_001363669.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.315

Variant links:

Genes affected

CALM1 (HGNC:1442): (calmodulin 1) This gene encodes one of three calmodulin proteins which are members of the EF-hand calcium-binding protein family. Calcium-induced activation of calmodulin regulates and modulates the function of cardiac ion channels. Two pseudogenes have been identified on chromosome 7 and X. Multiple transcript variants encoding different isoforms have been found for this gene.A missense mutation in the CALM1 gene has been associated with ventricular tachycardia.[provided by RefSeq, May 2020]

CALM1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BP6

Variant 14-90397013-C-T is Benign according to our data. Variant chr14-90397013-C-T is described in ClinVar as [Benign]. Clinvar id is 1164456.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CALM1	NM_001363669.2 link	c.-106+355C>T		intron_variant	Intron 1 of 5		NP_001350598.1
CALM1	NM_006888.6 link	c.-218C>T		upstream_gene_variant		ENST00000356978.9	NP_008819.1	P0DP23P0DP24P0DP25B4DJ51

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CALM1	ENST00000356978.9 link	c.-218C>T		upstream_gene_variant		1	NM_006888.6	ENSP00000349467.4		P0DP23

Frequencies

GnomAD3 genomes

AF:

0.404

AC:

61328

AN:

151836

Hom.:

14993

Cov.:

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.497

Gnomad AMR

AF:

0.375

Gnomad ASJ

AF:

0.491

Gnomad EAS

AF:

0.205

Gnomad SAS

AF:

0.390

Gnomad FIN

AF:

0.532

Gnomad MID

AF:

0.449

Gnomad NFE

AF:

0.561

Gnomad OTH

AF:

0.439

GnomAD4 exome

AF:

0.501

AC:

217872

AN:

434718

Hom.:

57433

Cov.:

AF XY:

0.496

AC XY:

114836

AN XY:

231530

show subpopulations

Gnomad4 AFR exome

AF:

0.151

Gnomad4 AMR exome

AF:

0.359

Gnomad4 ASJ exome

AF:

0.490

Gnomad4 EAS exome

AF:

0.282

Gnomad4 SAS exome

AF:

0.400

Gnomad4 FIN exome

AF:

0.537

Gnomad4 NFE exome

AF:

0.561

Gnomad4 OTH exome

AF:

0.486

GnomAD4 genome

AF:

0.404

AC:

61324

AN:

151950

Hom.:

14991

Cov.:

AF XY:

0.401

AC XY:

29774

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.139

Gnomad4 AMR

AF:

0.374

Gnomad4 ASJ

AF:

0.491

Gnomad4 EAS

AF:

0.206

Gnomad4 SAS

AF:

0.390

Gnomad4 FIN

AF:

0.532

Gnomad4 NFE

AF:

0.561

Gnomad4 OTH

AF:

0.436

Alfa

AF:

0.372

Hom.:

2102

Bravo

AF:

0.379

Asia WGS

AF:

0.262

AC:

909

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 15746150, 24205329) -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Catecholaminergic polymorphic ventricular tachycardia 4;C4015671:Long QT syndrome 14

Benign:1

Feb 03, 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

-0.38

CADD

Benign

8.2

DANN

Benign

0.86

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