chr1-107183121-C-A

Variant names:

• chr1-107183121-C-A
• rs4311917
• NM_001113226.3:c.246+34282C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001113226.3(NTNG1):​c.246+34282C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 152,110 control chromosomes in the GnomAD database, including 39,105 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 0.68 (39105 hom., cov: 32)
• Consequence: NTNG1 NM_001113226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.705

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NTNG1	NM_001113226.3	c.246+34282C>A		intron_variant	Intron 2 of 7	ENST00000370068.6	NP_001106697.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NTNG1	ENST00000370068.6	c.246+34282C>A		intron_variant	Intron 2 of 7	5	NM_001113226.3	ENSP00000359085.1

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102802 AN: 151992 Hom.: 39094 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.830

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.676 AC: 102835 AN: 152110 Hom.: 39105 Cov.: 32 AF XY: 0.679 AC XY: 50484 AN XY: 74354

African (AFR) AF: 0.293 AC: 12155 AN: 41472

American (AMR) AF: 0.715 AC: 10902 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3012 AN: 3470

East Asian (EAS) AF: 0.819 AC: 4228 AN: 5162

South Asian (SAS) AF: 0.796 AC: 3835 AN: 4818

European-Finnish (FIN) AF: 0.830 AC: 8810 AN: 10612

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.843 AC: 57366 AN: 68010

Other (OTH) AF: 0.716 AC: 1514 AN: 2114

Alfa AF: 0.792 Hom.: 80943

Bravo AF: 0.652

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	0.74
DANN	Benign	0.62
Mutation Taster		=100/0	polymorphism (auto)

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: rs4311917; hg19: chr1-107725743;