rs9962470

Positions:

• chr18-72797871-A-C
• chr18-72797871-A-G
• chr18-72797871-A-T

Variant summary

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

The NM_138966.5(NETO1):​c.470-3467T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,044 control chromosomes in the GnomAD database, including 40,405 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 0.72 (40405 hom., cov: 32)
• Consequence: NETO1 NM_138966.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.993

Genes affected

NETO1 (HGNC:13823): (neuropilin and tolloid like 1) This gene encodes a transmembrane protein containing two extracellular CUB domains followed by a low-density lipoprotein class A (LDLa) domain. This protein is thought to play a critical role in spatial learning and memory by regulating the function of synaptic N-methyl-D-aspartic acid receptor complexes in the hippocampus. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Aug 2017]

NETO1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NETO1	NM_138966.5	c.470-3467T>G		intron_variant		ENST00000327305.11	NP_620416.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NETO1	ENST00000327305.11	c.470-3467T>G		intron_variant		1	NM_138966.5	ENSP00000313088.6
NETO1	ENST00000583169.5	c.470-3467T>G		intron_variant		1		ENSP00000464312.1
NETO1	ENST00000579730.2	n.303-13965T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108678 AN: 151926 Hom.: 40380 Cov.: 32

Gnomad AFR AF: 0.516

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.715 AC: 108743 AN: 152044 Hom.: 40405 Cov.: 32 AF XY: 0.721 AC XY: 53577 AN XY: 74316

Gnomad4 AFR AF: 0.516

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.883

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.896

Gnomad4 FIN AF: 0.824

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.740

Alfa AF: 0.685 Hom.: 3848

Bravo AF: 0.688

Asia WGS AF: 0.879 AC: 3055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.49
DANN	Benign	0.62

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: rs9962470; hg19: chr18-70465106;