rs3131296

chr6-32205216-C-T

Variant summary

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

The NM_004557.4(NOTCH4):c.2866-827G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 151,500 control chromosomes in the GnomAD database, including 982 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 0.11 (982 hom., cov: 31)
• Consequence: NOTCH4 NM_004557.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703

Genes affected

NOTCH4 (HGNC:7884): (notch receptor 4) This gene encodes a member of the NOTCH family of proteins. Members of this Type I transmembrane protein family share structural characteristics including an extracellular domain consisting of multiple epidermal growth factor-like (EGF) repeats, and an intracellular domain consisting of multiple different domain types. Notch signaling is an evolutionarily conserved intercellular signaling pathway that regulates interactions between physically adjacent cells through binding of Notch family receptors to their cognate ligands. The encoded preproprotein is proteolytically processed in the trans-Golgi network to generate two polypeptide chains that heterodimerize to form the mature cell-surface receptor. This receptor may play a role in vascular, renal and hepatic development. Mutations in this gene may be associated with schizophrenia. Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that is proteolytically processed. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NOTCH4	NM_004557.4	c.2866-827G>A		intron_variant		ENST00000375023.3
NOTCH4	NR_134949.2	n.3107-827G>A		intron_variant, non_coding_transcript_variant
NOTCH4	NR_134950.2	n.3005-827G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NOTCH4	ENST00000375023.3	c.2866-827G>A		intron_variant		1	NM_004557.4	P1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16068 AN: 151386 Hom.: 982 Cov.: 31

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.0328

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.0910

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

GnomAD4 genome AF: 0.106 AC: 16065 AN: 151500 Hom.: 982 Cov.: 31 AF XY: 0.103 AC XY: 7625 AN XY: 73976

Gnomad4 AFR AF: 0.0912

Gnomad4 AMR AF: 0.0543

Gnomad4 ASJ AF: 0.0767

Gnomad4 EAS AF: 0.0331

Gnomad4 SAS AF: 0.0955

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.0900

Alfa AF: 0.128 Hom.: 2120

Bravo AF: 0.101

Asia WGS AF: 0.0550 AC: 193 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	8.2
Dann	Benign	0.49

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: rs3131296; hg19: chr6-32172993;