rs7214739

Variant names:

• chr17-9162618-T-C
• rs7214739
• NM_004822.3:c.1019-195T>C

Your query was ambiguous. Multiple possible variants found:

• chr17-9162618-T-C
• chr17-9162618-T-G

Variant summary

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

The NM_004822.3(NTN1):​c.1019-195T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,152 control chromosomes in the GnomAD database, including 38,339 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 0.71 (38339 hom., cov: 33)
• Consequence: NTN1 NM_004822.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTN1	NM_004822.3	c.1019-195T>C		intron_variant	Intron 2 of 6	ENST00000173229.7	NP_004813.2
NTN1	XM_006721595.4	c.1019-195T>C		intron_variant	Intron 2 of 6		XP_006721658.1
NTN1	XM_047437096.1	c.1019-195T>C		intron_variant	Intron 2 of 6		XP_047293052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NTN1	ENST00000173229.7	c.1019-195T>C		intron_variant	Intron 2 of 6	1	NM_004822.3	ENSP00000173229.2

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107735 AN: 152034 Hom.: 38309 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.709 AC: 107817 AN: 152152 Hom.: 38339 Cov.: 33 AF XY: 0.711 AC XY: 52861 AN XY: 74370

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.701

Alfa AF: 0.705 Hom.: 9127

Bravo AF: 0.710

Asia WGS AF: 0.732 AC: 2547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.1
DANN	Benign	0.60

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: rs7214739; hg19: chr17-9065935;