rs3785982

chr17-9186907-C-T

Variant summary

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

The NM_004822.3(NTN1):c.1411+3938C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0839 in 152,024 control chromosomes in the GnomAD database, including 743 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 0.084 (743 hom., cov: 32)
• Consequence: NTN1 NM_004822.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTN1	NM_004822.3	c.1411+3938C>T		intron_variant		ENST00000173229.7
NTN1	XM_006721595.4	c.1411+3938C>T		intron_variant
NTN1	XM_047437096.1	c.1411+3938C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTN1	ENST00000173229.7	c.1411+3938C>T		intron_variant		1	NM_004822.3	P1

Frequencies

GnomAD3 genomes AF: 0.0840 AC: 12754 AN: 151906 Hom.: 743 Cov.: 32

Gnomad AFR AF: 0.0204

Gnomad AMI AF: 0.0771

Gnomad AMR AF: 0.0837

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.0748

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

GnomAD4 genome AF: 0.0839 AC: 12762 AN: 152024 Hom.: 743 Cov.: 32 AF XY: 0.0859 AC XY: 6383 AN XY: 74292

Gnomad4 AFR AF: 0.0205

Gnomad4 AMR AF: 0.0835

Gnomad4 ASJ AF: 0.0752

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.0754

Alfa AF: 0.102 Hom.: 638

Bravo AF: 0.0791

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.0
Dann	Benign	0.46

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: rs3785982; hg19: chr17-9090224;