chr19-15192033-T-C

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000435.3(NOTCH3):c.606A>G(p.Ala202Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 1,613,208 control chromosomes in the GnomAD database, including 615,923 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.87 ( 57799 hom., cov: 34)

Exomes 𝑓: 0.87 ( 558124 hom. )

Consequence

NOTCH3
NM_000435.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:11

Conservation

PhyloP100: -3.47

Variant links:

Genes affected

NOTCH3 (HGNC:7883): (notch receptor 3) This gene encodes the third discovered human homologue of the Drosophilia melanogaster type I membrane protein notch. In Drosophilia, notch interaction with its cell-bound ligands (delta, serrate) establishes an intercellular signalling pathway that plays a key role in neural development. Homologues of the notch-ligands have also been identified in human, but precise interactions between these ligands and the human notch homologues remains to be determined. Mutations in NOTCH3 have been identified as the underlying cause of cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL). [provided by RefSeq, Jul 2008]

NOTCH3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 19-15192033-T-C is Benign according to our data. Variant chr19-15192033-T-C is described in ClinVar as [Benign]. Clinvar id is 256148.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-15192033-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-3.47 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOTCH3	NM_000435.3 link	c.606A>G	p.Ala202Ala	synonymous_variant	Exon 4 of 33	ENST00000263388.7	NP_000426.2	Q9UM47
NOTCH3	XM_005259924.5 link	c.606A>G	p.Ala202Ala	synonymous_variant	Exon 4 of 32		XP_005259981.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOTCH3	ENST00000263388.7 link	c.606A>G	p.Ala202Ala	synonymous_variant	Exon 4 of 33	1	NM_000435.3	ENSP00000263388.1		Q9UM47
NOTCH3	ENST00000601011.1 link	c.603A>G	p.Ala201Ala	synonymous_variant	Exon 4 of 23	5		ENSP00000473138.1		M0R3C9

Frequencies

GnomAD3 genomes

AF:

0.870

AC:

132353

AN:

152104

Hom.:

57761

Cov.:

show subpopulations

Gnomad AFR

AF:

0.907

Gnomad AMI

AF:

0.866

Gnomad AMR

AF:

0.763

Gnomad ASJ

AF:

0.878

Gnomad EAS

AF:

0.865

Gnomad SAS

AF:

0.834

Gnomad FIN

AF:

0.863

Gnomad MID

AF:

0.861

Gnomad NFE

AF:

0.876

Gnomad OTH

AF:

0.847

GnomAD3 exomes

AF:

0.848

AC:

212142

AN:

250060

Hom.:

90518

AF XY:

0.851

AC XY:

115350

AN XY:

135582

show subpopulations

Gnomad AFR exome

AF:

0.909

Gnomad AMR exome

AF:

0.701

Gnomad ASJ exome

AF:

0.871

Gnomad EAS exome

AF:

0.863

Gnomad SAS exome

AF:

0.840

Gnomad FIN exome

AF:

0.866

Gnomad NFE exome

AF:

0.879

Gnomad OTH exome

AF:

0.845

GnomAD4 exome

AF:

0.873

AC:

1275651

AN:

1460986

Hom.:

558124

Cov.:

AF XY:

0.872

AC XY:

633809

AN XY:

726822

show subpopulations

Gnomad4 AFR exome

AF:

0.908

Gnomad4 AMR exome

AF:

0.708

Gnomad4 ASJ exome

AF:

0.872

Gnomad4 EAS exome

AF:

0.880

Gnomad4 SAS exome

AF:

0.841

Gnomad4 FIN exome

AF:

0.866

Gnomad4 NFE exome

AF:

0.882

Gnomad4 OTH exome

AF:

0.860

GnomAD4 genome

AF:

0.870

AC:

132443

AN:

152222

Hom.:

57799

Cov.:

AF XY:

0.867

AC XY:

64511

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.907

Gnomad4 AMR

AF:

0.763

Gnomad4 ASJ

AF:

0.878

Gnomad4 EAS

AF:

0.866

Gnomad4 SAS

AF:

0.834

Gnomad4 FIN

AF:

0.863

Gnomad4 NFE

AF:

0.876

Gnomad4 OTH

AF:

0.844

Alfa

AF:

0.881

Hom.:

31239

Bravo

AF:

0.865

Asia WGS

AF:

0.837

AC:

2908

AN:

3478

EpiCase

AF:

0.872

EpiControl

AF:

0.867

ClinVar

Significance: Benign

Submissions summary: Benign:11

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Genome Diagnostics Laboratory, Amsterdam University Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided

Benign:4

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 14, 2021

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1

Benign:2

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Sep 05, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Lateral meningocele syndrome

Benign:1

Sep 05, 2021

Genome-Nilou Lab

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

-0.89

CADD

Benign

0.10

DANN

Benign

0.18

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