Variant chr1-201649136-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_001389617.1(NAV1):c.1329C>T(p.Gly443=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0727 in 1,611,722 control chromosomes in the GnomAD database, including 4,614 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.079 ( 526 hom., cov: 33)

Exomes 𝑓: 0.072 ( 4088 hom. )

Consequence

NAV1
NM_001389617.1 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.488

Variant links:

Genes affected

NAV1 (HGNC:15989): (neuron navigator 1) This gene belongs to the neuron navigator family and is expressed predominantly in the nervous system. The encoded protein contains coiled-coil domains and a conserved AAA domain characteristic for ATPases associated with a variety of cellular activities. This gene is similar to unc-53, a Caenorhabditis elegans gene involved in axon guidance. The exact function of this gene is not known, but it is thought to play a role in in neuronal development and regeneration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2009]

NAV1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 1-201649136-C-T is Benign according to our data. Variant chr1-201649136-C-T is described in ClinVar as [Benign]. Clinvar id is 1225724.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.488 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
NAV1	NM_001389617.1 linkuse as main transcript	c.1329C>T	p.Gly443=	synonymous_variant	5/34	ENST00000685211.1	NP_001376546.1
NAV1	NM_001389616.1 linkuse as main transcript	c.1329C>T	p.Gly443=	synonymous_variant	4/32		NP_001376545.1
NAV1	NM_001389615.1 linkuse as main transcript	c.1329C>T	p.Gly443=	synonymous_variant	5/31		NP_001376544.1
NAV1	NM_020443.5 linkuse as main transcript	c.468C>T	p.Gly156=	synonymous_variant	1/30		NP_065176.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAV1	ENST00000685211.1 linkuse as main transcript	c.1329C>T	p.Gly443=	synonymous_variant	5/34		NM_001389617.1	ENSP00000510803	P2
NAV1	ENST00000367296.8 linkuse as main transcript	c.468C>T	p.Gly156=	synonymous_variant	1/30	5		ENSP00000356265	A2	Q8NEY1-1
NAV1	ENST00000367302.5 linkuse as main transcript	c.507C>T	p.Gly169=	synonymous_variant	3/30	5		ENSP00000356271	A2

Frequencies

GnomAD3 genomes

AF:

0.0785

AC:

11949

AN:

152212

Hom.:

524

Cov.:

show subpopulations

Gnomad AFR

AF:

0.113

Gnomad AMI

AF:

0.0143

Gnomad AMR

AF:

0.0498

Gnomad ASJ

AF:

0.0980

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0513

Gnomad FIN

AF:

0.0428

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0776

Gnomad OTH

AF:

0.0755

GnomAD3 exomes

AF:

0.0615

AC:

14948

AN:

242966

Hom.:

543

AF XY:

0.0612

AC XY:

8114

AN XY:

132654

show subpopulations

Gnomad AFR exome

AF:

0.119

Gnomad AMR exome

AF:

0.0304

Gnomad ASJ exome

AF:

0.0914

Gnomad EAS exome

AF:

0.000776

Gnomad SAS exome

AF:

0.0508

Gnomad FIN exome

AF:

0.0420

Gnomad NFE exome

AF:

0.0777

Gnomad OTH exome

AF:

0.0598

GnomAD4 exome

AF:

0.0721

AC:

105271

AN:

1459392

Hom.:

4088

Cov.:

AF XY:

0.0717

AC XY:

52032

AN XY:

725894

show subpopulations

Gnomad4 AFR exome

AF:

0.120

Gnomad4 AMR exome

AF:

0.0326

Gnomad4 ASJ exome

AF:

0.0967

Gnomad4 EAS exome

AF:

0.000555

Gnomad4 SAS exome

AF:

0.0519

Gnomad4 FIN exome

AF:

0.0477

Gnomad4 NFE exome

AF:

0.0771

Gnomad4 OTH exome

AF:

0.0722

GnomAD4 genome

AF:

0.0785

AC:

11960

AN:

152330

Hom.:

526

Cov.:

AF XY:

0.0737

AC XY:

5491

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.112

Gnomad4 AMR

AF:

0.0497

Gnomad4 ASJ

AF:

0.0980

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.0510

Gnomad4 FIN

AF:

0.0428

Gnomad4 NFE

AF:

0.0776

Gnomad4 OTH

AF:

0.0790

Alfa

AF:

0.0801

Hom.:

184

Bravo

AF:

0.0796

Asia WGS

AF:

0.0330

AC:

116

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 17, 2020	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

DANN

Benign

0.89

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