Variant 1-107325019-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001113226.3(NTNG1):c.887+97C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0289 in 1,263,522 control chromosomes in the GnomAD database, including 714 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.024 ( 81 hom., cov: 32)

Exomes 𝑓: 0.030 ( 633 hom. )

Consequence

NTNG1
NM_001113226.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0670

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 1-107325019-C-T is Benign according to our data. Variant chr1-107325019-C-T is described in ClinVar as [Benign]. Clinvar id is 1274913.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0239 (3630/152200) while in subpopulation NFE AF= 0.0343 (2333/68012). AF 95% confidence interval is 0.0331. There are 81 homozygotes in gnomad4. There are 1861 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 81 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NTNG1	NM_001113226.3 link	c.887+97C>T		intron_variant		ENST00000370068.6	NP_001106697.1	Q9Y2I2-3Q5IEC8Q5IEC3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NTNG1	ENST00000370068.6 link	c.887+97C>T		intron_variant		5	NM_001113226.3	ENSP00000359085.1		Q9Y2I2-3

Frequencies

GnomAD3 genomes

AF:

0.0239

AC:

3632

AN:

152082

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00570

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.0196

Gnomad ASJ

AF:

0.00778

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00186

Gnomad FIN

AF:

0.0637

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0343

Gnomad OTH

AF:

0.0196

GnomAD4 exome

AF:

0.0296

AC:

32914

AN:

1111322

Hom.:

633

AF XY:

0.0287

AC XY:

15894

AN XY:

554254

show subpopulations

Gnomad4 AFR exome

AF:

0.00424

Gnomad4 AMR exome

AF:

0.0135

Gnomad4 ASJ exome

AF:

0.00952

Gnomad4 EAS exome

AF:

0.0000265

Gnomad4 SAS exome

AF:

0.00302

Gnomad4 FIN exome

AF:

0.0655

Gnomad4 NFE exome

AF:

0.0334

Gnomad4 OTH exome

AF:

0.0234

GnomAD4 genome

AF:

0.0239

AC:

3630

AN:

152200

Hom.:

Cov.:

AF XY:

0.0250

AC XY:

1861

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.00566

Gnomad4 AMR

AF:

0.0195

Gnomad4 ASJ

AF:

0.00778

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.0637

Gnomad4 NFE

AF:

0.0343

Gnomad4 OTH

AF:

0.0194

Alfa

AF:

0.0353

Hom.:

Bravo

AF:

0.0191

Asia WGS

AF:

0.00318

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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

-0.85

CADD

Benign

2.3

DANN

Benign

0.44

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