rs495198

chr1-201636988-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001389617.1(NAV1):c.826+7481G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 152,212 control chromosomes in the GnomAD database, including 49,971 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 (49971 hom., cov: 32)
• Consequence: NAV1 NM_001389617.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

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]

LOC124904482 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAV1	NM_001389617.1	c.826+7481G>A		intron_variant		ENST00000685211.1
LOC124904482	XR_007066789.1	n.10997C>T		non_coding_transcript_exon_variant	1/2
NAV1	NM_001389615.1	c.826+7481G>A		intron_variant
NAV1	NM_001389616.1	c.826+7481G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAV1	ENST00000685211.1	c.826+7481G>A		intron_variant			NM_001389617.1	P2
NAV1	ENST00000367302.5	c.4+7481G>A		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.809 AC: 122998 AN: 152094 Hom.: 49918 Cov.: 32

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.804

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.809 AC: 123106 AN: 152212 Hom.: 49971 Cov.: 32 AF XY: 0.803 AC XY: 59760 AN XY: 74420

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.799

Alfa AF: 0.822 Hom.: 15788

Bravo AF: 0.818

Asia WGS AF: 0.704 AC: 2450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.092
Dann	Benign	0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs495198; hg19: chr1-201606116;