rs9909240

Positions:

• chr17-9236774-G-A

Variant summary

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

The NM_004822.3(NTN1):​c.1487-2866G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 152,132 control chromosomes in the GnomAD database, including 20,574 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 0.50 (20574 hom., cov: 32)
• Consequence: NTN1 NM_004822.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

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]

LOC124903923 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NTN1	NM_004822.3	c.1487-2866G>A		intron_variant		ENST00000173229.7	NP_004813.2
LOC124903923	XR_007065614.1	n.10241G>A		non_coding_transcript_exon_variant	1/2
NTN1	XM_006721595.4	c.1487-2866G>A		intron_variant			XP_006721658.1
NTN1	XM_047437096.1	c.1487-2866G>A		intron_variant			XP_047293052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NTN1	ENST00000173229.7	c.1487-2866G>A		intron_variant		1	NM_004822.3	ENSP00000173229	P1

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75476 AN: 152016 Hom.: 20577 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.496 AC: 75494 AN: 152132 Hom.: 20574 Cov.: 32 AF XY: 0.488 AC XY: 36279 AN XY: 74372

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.494

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.516

Alfa AF: 0.606 Hom.: 15183

Bravo AF: 0.486

Asia WGS AF: 0.381 AC: 1326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.61

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: rs9909240; hg19: chr17-9140091; COSMIC: COSV51487990;