rs3815188

Positions:

Variant summary

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

The NM_000435.3(NOTCH3):c.303C>T(p.Thr101=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 1,611,970 control chromosomes in the GnomAD database, including 22,816 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2776 hom., cov: 31)

Exomes 𝑓: 0.16 ( 20040 hom. )

Consequence

NOTCH3
NM_000435.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:11O:1

Conservation

PhyloP100: 0.0660

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 19-15192414-G-A is Benign according to our data. Variant chr19-15192414-G-A is described in ClinVar as [Benign]. Clinvar id is 256131.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-15192414-G-A is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.066 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NOTCH3	NM_000435.3 linkuse as main transcript	c.303C>T	p.Thr101=	synonymous_variant	3/33	ENST00000263388.7	NP_000426.2
NOTCH3	XM_005259924.5 linkuse as main transcript	c.303C>T	p.Thr101=	synonymous_variant	3/32		XP_005259981.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NOTCH3	ENST00000263388.7 linkuse as main transcript	c.303C>T	p.Thr101=	synonymous_variant	3/33	1	NM_000435.3	ENSP00000263388	P1
NOTCH3	ENST00000601011.1 linkuse as main transcript	c.300C>T	p.Thr100=	synonymous_variant	3/23	5		ENSP00000473138

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27482

AN:

151884

Hom.:

2770

Cov.:

show subpopulations

Gnomad AFR

AF:

0.253

Gnomad AMI

AF:

0.113

Gnomad AMR

AF:

0.169

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.357

Gnomad SAS

AF:

0.143

Gnomad FIN

AF:

0.0850

Gnomad MID

AF:

0.188

Gnomad NFE

AF:

0.146

Gnomad OTH

AF:

0.162

GnomAD3 exomes

AF:

0.175

AC:

42778

AN:

244850

Hom.:

4131

AF XY:

0.169

AC XY:

22661

AN XY:

133984

show subpopulations

Gnomad AFR exome

AF:

0.260

Gnomad AMR exome

AF:

0.195

Gnomad ASJ exome

AF:

0.161

Gnomad EAS exome

AF:

0.345

Gnomad SAS exome

AF:

0.156

Gnomad FIN exome

AF:

0.0911

Gnomad NFE exome

AF:

0.152

Gnomad OTH exome

AF:

0.161

GnomAD4 exome

AF:

0.159

AC:

232591

AN:

1459970

Hom.:

20040

Cov.:

AF XY:

0.158

AC XY:

115115

AN XY:

726318

show subpopulations

Gnomad4 AFR exome

AF:

0.263

Gnomad4 AMR exome

AF:

0.195

Gnomad4 ASJ exome

AF:

0.161

Gnomad4 EAS exome

AF:

0.376

Gnomad4 SAS exome

AF:

0.156

Gnomad4 FIN exome

AF:

0.0913

Gnomad4 NFE exome

AF:

0.150

Gnomad4 OTH exome

AF:

0.165

GnomAD4 genome

AF:

0.181

AC:

27513

AN:

152000

Hom.:

2776

Cov.:

AF XY:

0.178

AC XY:

13246

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.253

Gnomad4 AMR

AF:

0.169

Gnomad4 ASJ

AF:

0.175

Gnomad4 EAS

AF:

0.358

Gnomad4 SAS

AF:

0.142

Gnomad4 FIN

AF:

0.0850

Gnomad4 NFE

AF:

0.146

Gnomad4 OTH

AF:

0.161

Alfa

AF:

0.152

Hom.:

3172

Bravo

AF:

0.194

Asia WGS

AF:

0.245

AC:

848

AN:

3478

EpiCase

AF:

0.153

EpiControl

AF:

0.156

ClinVar

Significance: Benign

Submissions summary: Benign:11Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jul 12, 2017	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -

not provided

Benign:4

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jan 04, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 12, 2021	This variant is associated with the following publications: (PMID: 16949066, 31288479, 10371548, 21616505, 22153900) -

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

Benign:2Other:1

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Sep 05, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	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. -
not provided, no classification provided	phenotyping only	GenomeConnect - CureCADASIL	-	Variant interpreted as Benign and reported on 06-21-2005 by Lab or GTR ID 1012. GenomeConnect-CureCADASIL assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. -

Lateral meningocele syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

1.6

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