rs10404382

Positions:

• chr19-15190578-C-A
• chr19-15190578-C-G
• chr19-15190578-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000435.3(NOTCH3):​c.1036+846G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 152,106 control chromosomes in the GnomAD database, including 57,636 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.87 (57636 hom., cov: 31)
• Consequence: NOTCH3 NM_000435.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• 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/exons	MANE	Protein	UniProt
NOTCH3	NM_000435.3	c.1036+846G>T		intron_variant		ENST00000263388.7	NP_000426.2
NOTCH3	XM_005259924.5	c.1036+846G>T		intron_variant			XP_005259981.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NOTCH3	ENST00000263388.7	c.1036+846G>T		intron_variant		1	NM_000435.3	ENSP00000263388.1
NOTCH3	ENST00000601011.1	c.1033+846G>T		intron_variant		5		ENSP00000473138.1

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132102 AN: 151988 Hom.: 57599 Cov.: 31

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.844

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.869 AC: 132190 AN: 152106 Hom.: 57636 Cov.: 31 AF XY: 0.866 AC XY: 64356 AN XY: 74338

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.876

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.862

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.841

Alfa AF: 0.873 Hom.: 26668

Bravo AF: 0.864

Asia WGS AF: 0.832 AC: 2892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.40

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

Other links and lift over

dbSNP: rs10404382; hg19: chr19-15301389;