Variant chr9-132198490-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_032536.4(NTNG2):c.738C>T(p.Phe246=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 1,612,962 control chromosomes in the GnomAD database, including 81,327 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 6557 hom., cov: 33)

Exomes 𝑓: 0.32 ( 74770 hom. )

Consequence

NTNG2
NM_032536.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 2.74

Variant links:

Genes affected

NTNG2 (HGNC:14288): (netrin G2) Predicted to be involved in several processes, including basement membrane assembly; cell morphogenesis involved in differentiation; and regulation of cell projection organization. Located in Flemming body; intercellular bridge; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

NTNG2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant 9-132198490-C-T is Benign according to our data. Variant chr9-132198490-C-T is described in ClinVar as [Benign]. Clinvar id is 1222197.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.74 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NTNG2	NM_032536.4 linkuse as main transcript	c.738C>T	p.Phe246=	synonymous_variant	3/8	ENST00000393229.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NTNG2	ENST00000393229.4 linkuse as main transcript	c.738C>T	p.Phe246=	synonymous_variant	3/8	1	NM_032536.4	P1	Q96CW9-1

Frequencies

GnomAD3 genomes

AF:

0.287

AC:

43606

AN:

152074

Hom.:

6560

Cov.:

show subpopulations

Gnomad AFR

AF:

0.200

Gnomad AMI

AF:

0.254

Gnomad AMR

AF:

0.275

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.359

Gnomad SAS

AF:

0.319

Gnomad FIN

AF:

0.395

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.314

Gnomad OTH

AF:

0.297

GnomAD3 exomes

AF:

0.320

AC:

79560

AN:

248472

Hom.:

13111

AF XY:

0.324

AC XY:

43811

AN XY:

135114

show subpopulations

Gnomad AFR exome

AF:

0.193

Gnomad AMR exome

AF:

0.295

Gnomad ASJ exome

AF:

0.374

Gnomad EAS exome

AF:

0.356

Gnomad SAS exome

AF:

0.335

Gnomad FIN exome

AF:

0.390

Gnomad NFE exome

AF:

0.318

Gnomad OTH exome

AF:

0.320

GnomAD4 exome

AF:

0.318

AC:

464708

AN:

1460770

Hom.:

74770

Cov.:

AF XY:

0.320

AC XY:

232336

AN XY:

726710

show subpopulations

Gnomad4 AFR exome

AF:

0.197

Gnomad4 AMR exome

AF:

0.295

Gnomad4 ASJ exome

AF:

0.373

Gnomad4 EAS exome

AF:

0.383

Gnomad4 SAS exome

AF:

0.334

Gnomad4 FIN exome

AF:

0.384

Gnomad4 NFE exome

AF:

0.315

Gnomad4 OTH exome

AF:

0.308

GnomAD4 genome

AF:

0.287

AC:

43616

AN:

152192

Hom.:

6557

Cov.:

AF XY:

0.290

AC XY:

21595

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.200

Gnomad4 AMR

AF:

0.275

Gnomad4 ASJ

AF:

0.358

Gnomad4 EAS

AF:

0.358

Gnomad4 SAS

AF:

0.319

Gnomad4 FIN

AF:

0.395

Gnomad4 NFE

AF:

0.314

Gnomad4 OTH

AF:

0.295

Alfa

AF:

0.315

Hom.:

18130

Bravo

AF:

0.276

Asia WGS

AF:

0.322

AC:

1117

AN:

3478

EpiCase

AF:

0.319

EpiControl

AF:

0.334

ClinVar

Significance: Benign

Submissions summary: Benign:3

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	Nov 20, 2018	- -

Neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotonia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

DANN

Benign

0.80

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