rs628117

Positions:

• chr1-107454484-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.1390+17685C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,772 control chromosomes in the GnomAD database, including 24,075 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 0.56 (24075 hom., cov: 31)
• Consequence: NTNG1 NM_001113226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.61

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NTNG1	NM_001113226.3	c.1390+17685C>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.1390+17685C>T		intron_variant		5	NM_001113226.3	ENSP00000359085	P1

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84994 AN: 151654 Hom.: 24065 Cov.: 31

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.560 AC: 85054 AN: 151772 Hom.: 24075 Cov.: 31 AF XY: 0.560 AC XY: 41522 AN XY: 74124

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.584

Alfa AF: 0.571 Hom.: 33653

Bravo AF: 0.570

Asia WGS AF: 0.647 AC: 2248 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0020
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: rs628117; hg19: chr1-107997106;