chr1-107394846-C-G

Position:

• chr1-107394846-C-G

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.888-308C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,076 control chromosomes in the GnomAD database, including 1,572 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.14 (1572 hom., cov: 32)
• Consequence: NTNG1 NM_001113226.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.36

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=-0.91).
• BP6: Variant 1-107394846-C-G is Benign according to our data. Variant chr1-107394846-C-G is described in ClinVar as [Benign]. Clinvar id is 1225825.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTNG1	NM_001113226.3	c.888-308C>G		intron_variant		ENST00000370068.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTNG1	ENST00000370068.6	c.888-308C>G		intron_variant		5	NM_001113226.3	P1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20893 AN: 151958 Hom.: 1573 Cov.: 32

Gnomad AFR AF: 0.0977

Gnomad AMI AF: 0.0681

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.137 AC: 20892 AN: 152076 Hom.: 1572 Cov.: 32 AF XY: 0.135 AC XY: 10041 AN XY: 74328

Gnomad4 AFR AF: 0.0977

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.0209

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.145

Alfa AF: 0.0419 Hom.: 35

Bravo AF: 0.142

Asia WGS AF: 0.105 AC: 364 AN: 3478

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 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.39

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: rs12754483; hg19: chr1-107937468;