rs10494067

chr1-107288236-A-Cchr1-107288236-A-Gchr1-107288236-A-T

Variant summary

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

The NM_001113226.3(NTNG1):c.247-36046A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0409 in 152,278 control chromosomes in the GnomAD database, including 158 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 0.041 (158 hom., cov: 32)
• Consequence: NTNG1 NM_001113226.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTNG1	NM_001113226.3	c.247-36046A>C		intron_variant		ENST00000370068.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTNG1	ENST00000370068.6	c.247-36046A>C		intron_variant		5	NM_001113226.3	P1

Frequencies

GnomAD3 genomes AF: 0.0410 AC: 6231 AN: 152160 Hom.: 158 Cov.: 32

Gnomad AFR AF: 0.0118

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.0772

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0431

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0574

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0409 AC: 6235 AN: 152278 Hom.: 158 Cov.: 32 AF XY: 0.0404 AC XY: 3010 AN XY: 74466

Gnomad4 AFR AF: 0.0117

Gnomad4 AMR AF: 0.0354

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.0775

Gnomad4 SAS AF: 0.0462

Gnomad4 FIN AF: 0.0431

Gnomad4 NFE AF: 0.0574

Gnomad4 OTH AF: 0.0392

Alfa AF: 0.0522 Hom.: 495

Bravo AF: 0.0394

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.087
Dann	Benign	0.47

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: rs10494067; hg19: chr1-107830858;