Variant chr1-1916569-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_138705.4(CALML6):c.207C>T(p.Pro69Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00138 in 1,611,726 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0014 ( 1 hom., cov: 31)

Exomes 𝑓: 0.0014 ( 5 hom. )

Consequence

CALML6
NM_138705.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.494

Variant links:

Genes affected

CALML6 (HGNC:24193): (calmodulin like 6) Predicted to enable calcium ion binding activity and enzyme regulator activity. Predicted to be involved in regulation of catalytic activity. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

CALML6 links:

CALML6 (HGNC:):

CALML6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BP6

Variant 1-1916569-C-T is Benign according to our data. Variant chr1-1916569-C-T is described in ClinVar as [Benign]. Clinvar id is 781580.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CALML6	NM_138705.4 linkuse as main transcript	c.207C>T	p.Pro69Pro	synonymous_variant	3/6	ENST00000307786.8	NP_619650.2	Q8TD86
CALML6	NM_001330313.2 linkuse as main transcript	c.156C>T	p.Pro52Pro	synonymous_variant	2/5		NP_001317242.1	B1AKR1
CALML6	XM_005244729.4 linkuse as main transcript	c.273C>T	p.Pro91Pro	synonymous_variant	3/6		XP_005244786.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
CALML6	ENST00000307786.8 linkuse as main transcript	c.207C>T	p.Pro69Pro	synonymous_variant	3/6	1	NM_138705.4	ENSP00000304643.3	Q8TD86
CALML6	ENST00000378604.3 linkuse as main transcript	c.156C>T	p.Pro52Pro	synonymous_variant	2/5	3		ENSP00000367867.3	B1AKR1
CALML6	ENST00000482402.1 linkuse as main transcript	n.1304C>T		non_coding_transcript_exon_variant	1/3	2
CALML6	ENST00000462293.1 linkuse as main transcript	n.328-183C>T		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00138

AC:

209

AN:

151912

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000411

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00105

Gnomad ASJ

AF:

0.0144

Gnomad EAS

AF:

0.000387

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.000662

Gnomad MID

AF:

0.00637

Gnomad NFE

AF:

0.00144

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00177

AC:

440

AN:

248268

Hom.:

AF XY:

0.00192

AC XY:

259

AN XY:

134580

show subpopulations

Gnomad AFR exome

AF:

0.0000624

Gnomad AMR exome

AF:

0.00114

Gnomad ASJ exome

AF:

0.0142

Gnomad EAS exome

AF:

0.0000546

Gnomad SAS exome

AF:

0.00148

Gnomad FIN exome

AF:

0.000372

Gnomad NFE exome

AF:

0.00166

Gnomad OTH exome

AF:

0.00331

GnomAD4 exome

AF:

0.00138

AC:

2011

AN:

1459694

Hom.:

Cov.:

AF XY:

0.00146

AC XY:

1060

AN XY:

726046

show subpopulations

Gnomad4 AFR exome

AF:

0.000180

Gnomad4 AMR exome

AF:

0.00115

Gnomad4 ASJ exome

AF:

0.0145

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00156

Gnomad4 FIN exome

AF:

0.000568

Gnomad4 NFE exome

AF:

0.00110

Gnomad4 OTH exome

AF:

0.00244

GnomAD4 genome

AF:

0.00137

AC:

209

AN:

152032

Hom.:

Cov.:

AF XY:

0.00141

AC XY:

105

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.000410

Gnomad4 AMR

AF:

0.00105

Gnomad4 ASJ

AF:

0.0144

Gnomad4 EAS

AF:

0.000388

Gnomad4 SAS

AF:

0.00208

Gnomad4 FIN

AF:

0.000662

Gnomad4 NFE

AF:

0.00144

Gnomad4 OTH

AF:

0.00332

Alfa

AF:

0.00230

Hom.:

Bravo

AF:

0.00134

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.00256

EpiControl

AF:

0.00297

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Apr 24, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

DANN

Benign

0.89

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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