rs9788972

Variant names:

• chr17-9016313-G-A
• rs9788972
• XM_047437096.1:c.-63-5998G>A

Your query was ambiguous. Multiple possible variants found:

• chr17-9016313-G-A
• chr17-9016313-G-C

Variant summary

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

The XM_047437096.1(NTN1):​c.-63-5998G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,850 control chromosomes in the GnomAD database, including 6,336 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 0.29 (6336 hom., cov: 31)
• Consequence: NTN1 XM_047437096.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481

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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTN1	XM_047437096.1	c.-63-5998G>A		intron_variant	Intron 1 of 6		XP_047293052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43378 AN: 151730 Hom.: 6334 Cov.: 31

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.286 AC: 43411 AN: 151850 Hom.: 6336 Cov.: 31 AF XY: 0.291 AC XY: 21564 AN XY: 74202

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.271

Alfa AF: 0.284 Hom.: 12578

Bravo AF: 0.283

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9788972; hg19: chr17-8919630;