rs940850

chr17-9026763-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_004822.3(NTN1):c.1018+3372C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 151,678 control chromosomes in the GnomAD database, including 1,187 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 (1187 hom., cov: 31)
• Consequence: NTN1 NM_004822.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.58

Genes affected

NTN1 (HGNC:8029): (netrin 1) Netrin is included in a family of laminin-related secreted proteins. The function of this gene has not yet been defined; however, netrin is thought to be involved in axon guidance and cell migration during development. Mutations and loss of expression of netrin suggest that variation in netrin may be involved in cancer development. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTN1	NM_004822.3	c.1018+3372C>T		intron_variant		ENST00000173229.7
NTN1	XM_006721595.4	c.1018+3372C>T		intron_variant
NTN1	XM_047437096.1	c.1018+3372C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTN1	ENST00000173229.7	c.1018+3372C>T		intron_variant		1	NM_004822.3	P1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17243 AN: 151560 Hom.: 1174 Cov.: 31

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.0613

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0990

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.114 AC: 17292 AN: 151678 Hom.: 1187 Cov.: 31 AF XY: 0.115 AC XY: 8541 AN XY: 74070

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.0660

Gnomad4 EAS AF: 0.256

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.0613

Gnomad4 NFE AF: 0.0990

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0997 Hom.: 815

Bravo AF: 0.118

Asia WGS AF: 0.201 AC: 696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
Cadd	Benign	19
Dann	Benign	0.84

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: rs940850; hg19: chr17-8930080;