rs10521156

chr17-9039413-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.1018+16022G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,066 control chromosomes in the GnomAD database, including 2,434 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 0.17 (2434 hom., cov: 32)
• Consequence: NTN1 NM_004822.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTN1	NM_004822.3	c.1018+16022G>A		intron_variant		ENST00000173229.7
NTN1	XM_006721595.4	c.1018+16022G>A		intron_variant
NTN1	XM_047437096.1	c.1018+16022G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTN1	ENST00000173229.7	c.1018+16022G>A		intron_variant		1	NM_004822.3	P1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25878 AN: 151948 Hom.: 2437 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0511

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.170 AC: 25889 AN: 152066 Hom.: 2434 Cov.: 32 AF XY: 0.166 AC XY: 12373 AN XY: 74340

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0508

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.159

Alfa AF: 0.166 Hom.: 939

Bravo AF: 0.166

Asia WGS AF: 0.0340 AC: 119 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.6
Dann	Benign	0.57

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: rs10521156; hg19: chr17-8942730;