rs17505688

chr1-107156419-T-C

Variant summary

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

The NM_001113226.3(NTNG1):c.246+7580T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 152,166 control chromosomes in the GnomAD database, including 257 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 0.051 (257 hom., cov: 32)
• Consequence: NTNG1 NM_001113226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTNG1	NM_001113226.3	c.246+7580T>C		intron_variant		ENST00000370068.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTNG1	ENST00000370068.6	c.246+7580T>C		intron_variant		5	NM_001113226.3	P1

Frequencies

GnomAD3 genomes AF: 0.0509 AC: 7744 AN: 152048 Hom.: 257 Cov.: 32

Gnomad AFR AF: 0.0146

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0401

Gnomad ASJ AF: 0.0242

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.0419

Gnomad FIN AF: 0.0794

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0772

Gnomad OTH AF: 0.0508

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

GnomAD4 genome AF: 0.0509 AC: 7744 AN: 152166 Hom.: 257 Cov.: 32 AF XY: 0.0501 AC XY: 3728 AN XY: 74382

Gnomad4 AFR AF: 0.0146

Gnomad4 AMR AF: 0.0402

Gnomad4 ASJ AF: 0.0242

Gnomad4 EAS AF: 0.00347

Gnomad4 SAS AF: 0.0419

Gnomad4 FIN AF: 0.0794

Gnomad4 NFE AF: 0.0772

Gnomad4 OTH AF: 0.0498

Alfa AF: 0.0680 Hom.: 176

Bravo AF: 0.0463

Asia WGS AF: 0.0220 AC: 78 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.4
Dann	Benign	0.34

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: rs17505688; hg19: chr1-107699041;