1-107325095-A-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001113226.3(NTNG1):c.887+173A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 151,910 control chromosomes in the GnomAD database, including 24,042 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.54 (24042 hom., cov: 32)
• Consequence: NTNG1 NM_001113226.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.228

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 1-107325095-A-C is Benign according to our data. Variant chr1-107325095-A-C is described in ClinVar as [Benign]. Clinvar id is 1234257.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTNG1	NM_001113226.3	c.887+173A>C		intron_variant		ENST00000370068.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTNG1	ENST00000370068.6	c.887+173A>C		intron_variant		5	NM_001113226.3	P1

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82655 AN: 151792 Hom.: 24039 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.544 AC: 82692 AN: 151910 Hom.: 24042 Cov.: 32 AF XY: 0.550 AC XY: 40808 AN XY: 74244

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.558

Alfa AF: 0.588 Hom.: 4280

Bravo AF: 0.528

Asia WGS AF: 0.504 AC: 1750 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.68
Dann	Benign	0.40

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: rs1132933; hg19: chr1-107867717; COSMIC: COSV53981512;