rs5023291

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001113226.3(NTNG1):​c.246+30116C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 152,132 control chromosomes in the GnomAD database, including 49,693 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 0.81 ( 49693 hom., cov: 32)

Consequence

NTNG1
NM_001113226.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.325
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NTNG1NM_001113226.3 linkuse as main transcriptc.246+30116C>A intron_variant ENST00000370068.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NTNG1ENST00000370068.6 linkuse as main transcriptc.246+30116C>A intron_variant 5 NM_001113226.3 P1Q9Y2I2-3

Frequencies

GnomAD3 genomes
AF:
0.807
AC:
122686
AN:
152014
Hom.:
49662
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.747
Gnomad AMI
AF:
0.839
Gnomad AMR
AF:
0.763
Gnomad ASJ
AF:
0.869
Gnomad EAS
AF:
0.817
Gnomad SAS
AF:
0.798
Gnomad FIN
AF:
0.831
Gnomad MID
AF:
0.870
Gnomad NFE
AF:
0.845
Gnomad OTH
AF:
0.821
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.807
AC:
122767
AN:
152132
Hom.:
49693
Cov.:
32
AF XY:
0.805
AC XY:
59848
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.747
Gnomad4 AMR
AF:
0.762
Gnomad4 ASJ
AF:
0.869
Gnomad4 EAS
AF:
0.817
Gnomad4 SAS
AF:
0.800
Gnomad4 FIN
AF:
0.831
Gnomad4 NFE
AF:
0.845
Gnomad4 OTH
AF:
0.822
Alfa
AF:
0.827
Hom.:
6475
Bravo
AF:
0.799
Asia WGS
AF:
0.786
AC:
2733
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.64
DANN
Benign
0.63

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.

Other links and lift over

dbSNP: rs5023291; hg19: chr1-107721577; API