6-32222064-T-G

Variant names:

• chr6-32222064-T-G
• rs715299
• NM_004557.4:c.451+447A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004557.4(NOTCH4):​c.451+447A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,860 control chromosomes in the GnomAD database, including 10,367 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 0.36 (10367 hom., cov: 31)
• Consequence: NOTCH4 NM_004557.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 19 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOTCH4	NM_004557.4	c.451+447A>C		intron_variant	Intron 3 of 29	ENST00000375023.3	NP_004548.3
NOTCH4	NR_134949.2	n.590+447A>C		intron_variant	Intron 3 of 29
NOTCH4	NR_134950.2	n.590+447A>C		intron_variant	Intron 3 of 28

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOTCH4	ENST00000375023.3	c.451+447A>C		intron_variant	Intron 3 of 29	1	NM_004557.4	ENSP00000364163.3
NOTCH4	ENST00000473562.1	n.580+447A>C		intron_variant	Intron 3 of 10	1

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54140 AN: 151742 Hom.: 10357 Cov.: 31

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.357 AC: 54189 AN: 151860 Hom.: 10367 Cov.: 31 AF XY: 0.352 AC XY: 26165 AN XY: 74244

African (AFR) AF: 0.460 AC: 19045 AN: 41400

American (AMR) AF: 0.300 AC: 4591 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1252 AN: 3464

East Asian (EAS) AF: 0.610 AC: 3119 AN: 5110

South Asian (SAS) AF: 0.410 AC: 1973 AN: 4810

European-Finnish (FIN) AF: 0.221 AC: 2336 AN: 10560

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20810 AN: 67918

Other (OTH) AF: 0.364 AC: 768 AN: 2112

Alfa AF: 0.322 Hom.: 7696

Bravo AF: 0.372

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.7
DANN	Benign	0.86
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs715299; hg19: chr6-32189841;