19-15174241-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.4563A>G(p.Pro1521Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.893 in 1,595,316 control chromosomes in the GnomAD database, including 637,948 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.90 ( 62274 hom., cov: 34)

Exomes 𝑓: 0.89 ( 575674 hom. )

Consequence

NOTCH3
NM_000435.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -4.37

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=-0.77).

BP6

Variant 19-15174241-T-C is Benign according to our data. Variant chr19-15174241-T-C is described in ClinVar as [Benign]. Clinvar id is 256138.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-15174241-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-4.37 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOTCH3	NM_000435.3 link	c.4563A>G	p.Pro1521Pro	synonymous_variant	Exon 25 of 33	ENST00000263388.7	NP_000426.2	Q9UM47
NOTCH3	XM_005259924.5 link	c.4407A>G	p.Pro1469Pro	synonymous_variant	Exon 24 of 32		XP_005259981.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOTCH3	ENST00000263388.7 link	c.4563A>G	p.Pro1521Pro	synonymous_variant	Exon 25 of 33	1	NM_000435.3	ENSP00000263388.1		Q9UM47

Frequencies

GnomAD3 genomes

AF:

0.902

AC:

137252

AN:

152178

Hom.:

62222

Cov.:

show subpopulations

Gnomad AFR

AF:

0.977

Gnomad AMI

AF:

0.885

Gnomad AMR

AF:

0.782

Gnomad ASJ

AF:

0.876

Gnomad EAS

AF:

0.805

Gnomad SAS

AF:

0.857

Gnomad FIN

AF:

0.883

Gnomad MID

AF:

0.886

Gnomad NFE

AF:

0.899

Gnomad OTH

AF:

0.879

GnomAD3 exomes

AF:

0.863

AC:

185645

AN:

215228

Hom.:

80509

AF XY:

0.866

AC XY:

102922

AN XY:

118884

show subpopulations

Gnomad AFR exome

AF:

0.980

Gnomad AMR exome

AF:

0.718

Gnomad ASJ exome

AF:

0.872

Gnomad EAS exome

AF:

0.801

Gnomad SAS exome

AF:

0.860

Gnomad FIN exome

AF:

0.886

Gnomad NFE exome

AF:

0.900

Gnomad OTH exome

AF:

0.860

GnomAD4 exome

AF:

0.892

AC:

1287588

AN:

1443020

Hom.:

575674

Cov.:

AF XY:

0.891

AC XY:

639275

AN XY:

717490

show subpopulations

Gnomad4 AFR exome

AF:

0.981

Gnomad4 AMR exome

AF:

0.724

Gnomad4 ASJ exome

AF:

0.871

Gnomad4 EAS exome

AF:

0.827

Gnomad4 SAS exome

AF:

0.859

Gnomad4 FIN exome

AF:

0.886

Gnomad4 NFE exome

AF:

0.903

Gnomad4 OTH exome

AF:

0.879

GnomAD4 genome

AF:

0.902

AC:

137362

AN:

152296

Hom.:

62274

Cov.:

AF XY:

0.898

AC XY:

66849

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.977

Gnomad4 AMR

AF:

0.782

Gnomad4 ASJ

AF:

0.876

Gnomad4 EAS

AF:

0.805

Gnomad4 SAS

AF:

0.857

Gnomad4 FIN

AF:

0.883

Gnomad4 NFE

AF:

0.899

Gnomad4 OTH

AF:

0.880

Alfa

AF:

0.897

Hom.:

22307

Bravo

AF:

0.896

Asia WGS

AF:

0.854

AC:

2969

AN:

3478

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

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 27, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 14, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 29544907) -

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

-0.77

CADD

Benign

0.15

DANN

Benign

0.67

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