Variant chr1-107418537-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_001113226.3(NTNG1):c.1087+10829A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 1,374,710 control chromosomes in the GnomAD database, including 17,043 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 1720 hom., cov: 32)

Exomes 𝑓: 0.15 ( 15323 hom. )

Consequence

NTNG1
NM_001113226.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.401

Variant links:

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]

NTNG1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.32).

BP6

Variant 1-107418537-A-G is Benign according to our data. Variant chr1-107418537-A-G is described in ClinVar as [Benign]. Clinvar id is 1250495.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTNG1	NM_001113226.3 linkuse as main transcript	c.1087+10829A>G		intron_variant		ENST00000370068.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTNG1	ENST00000370068.6 linkuse as main transcript	c.1087+10829A>G		intron_variant		5	NM_001113226.3	P1	Q9Y2I2-3

Frequencies

GnomAD3 genomes

AF:

0.146

AC:

22201

AN:

151834

Hom.:

1721

Cov.:

show subpopulations

Gnomad AFR

AF:

0.128

Gnomad AMI

AF:

0.0680

Gnomad AMR

AF:

0.178

Gnomad ASJ

AF:

0.190

Gnomad EAS

AF:

0.0210

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.161

Gnomad OTH

AF:

0.151

GnomAD3 exomes

AF:

0.151

AC:

25689

AN:

170122

Hom.:

2119

AF XY:

0.150

AC XY:

13549

AN XY:

90328

show subpopulations

Gnomad AFR exome

AF:

0.127

Gnomad AMR exome

AF:

0.194

Gnomad ASJ exome

AF:

0.195

Gnomad EAS exome

AF:

0.0198

Gnomad SAS exome

AF:

0.151

Gnomad FIN exome

AF:

0.125

Gnomad NFE exome

AF:

0.166

Gnomad OTH exome

AF:

0.168

GnomAD4 exome

AF:

0.154

AC:

188104

AN:

1222758

Hom.:

15323

Cov.:

AF XY:

0.154

AC XY:

94308

AN XY:

612188

show subpopulations

Gnomad4 AFR exome

AF:

0.124

Gnomad4 AMR exome

AF:

0.192

Gnomad4 ASJ exome

AF:

0.192

Gnomad4 EAS exome

AF:

0.0306

Gnomad4 SAS exome

AF:

0.145

Gnomad4 FIN exome

AF:

0.123

Gnomad4 NFE exome

AF:

0.160

Gnomad4 OTH exome

AF:

0.154

GnomAD4 genome

AF:

0.146

AC:

22205

AN:

151952

Hom.:

1720

Cov.:

AF XY:

0.144

AC XY:

10659

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.128

Gnomad4 AMR

AF:

0.179

Gnomad4 ASJ

AF:

0.190

Gnomad4 EAS

AF:

0.0209

Gnomad4 SAS

AF:

0.149

Gnomad4 FIN

AF:

0.123

Gnomad4 NFE

AF:

0.161

Gnomad4 OTH

AF:

0.150

Alfa

AF:

0.160

Hom.:

1088

Bravo

AF:

0.151

Asia WGS

AF:

0.107

AC:

371

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

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

-0.32

CADD

Benign

DANN

Benign

0.67

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over