rs17509160

Positions:

• chr1-107312391-C-T

Variant summary

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

The NM_001113226.3(NTNG1):​c.247-11891C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.073 in 152,108 control chromosomes in the GnomAD database, including 621 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 0.073 (621 hom., cov: 32)
• Consequence: NTNG1 NM_001113226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.101

Genes affected

NTNG1 (HGNC:23319): (netrin G1) This gene encodes a preproprotein that is processed into a secreted protein containing eukaroytic growth factor (EGF)-like domains. This protein acts to guide axon growth during neuronal development. Polymorphisms in this gene may be associated with schizophrenia. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Aug 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NTNG1	NM_001113226.3	c.247-11891C>T		intron_variant		ENST00000370068.6	NP_001106697.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NTNG1	ENST00000370068.6	c.247-11891C>T		intron_variant		5	NM_001113226.3	ENSP00000359085	P1

Frequencies

GnomAD3 genomes AF: 0.0730 AC: 11102 AN: 151992 Hom.: 624 Cov.: 32

Gnomad AFR AF: 0.0156

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.0819

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.0757

Gnomad OTH AF: 0.0860

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

GnomAD4 genome AF: 0.0730 AC: 11098 AN: 152108 Hom.: 621 Cov.: 32 AF XY: 0.0773 AC XY: 5747 AN XY: 74334

Gnomad4 AFR AF: 0.0155

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.0819

Gnomad4 NFE AF: 0.0757

Gnomad4 OTH AF: 0.0866

Alfa AF: 0.0786 Hom.: 562

Bravo AF: 0.0756

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.94
DANN	Benign	0.65

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: rs17509160; hg19: chr1-107855013;