1-201661333-T-G

Variant summary

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

The NM_001389617.1(NAV1):c.1618+11908T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 152,044 control chromosomes in the GnomAD database, including 6,945 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 0.28 (6945 hom., cov: 32)
• Consequence: NAV1 NM_001389617.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAV1	NM_001389617.1	c.1618+11908T>G		intron_variant		ENST00000685211.1
NAV1	NM_001389615.1	c.1618+11908T>G		intron_variant
NAV1	NM_001389616.1	c.1618+11908T>G		intron_variant
NAV1	NM_020443.5	c.757+11908T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAV1	ENST00000685211.1	c.1618+11908T>G		intron_variant			NM_001389617.1	P2
NAV1	ENST00000367296.8	c.757+11908T>G		intron_variant		5		A2
NAV1	ENST00000367302.5	c.796+11908T>G		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43204 AN: 151924 Hom.: 6940 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.284 AC: 43213 AN: 152044 Hom.: 6945 Cov.: 32 AF XY: 0.291 AC XY: 21651 AN XY: 74296

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.318

Alfa AF: 0.306 Hom.: 9107

Bravo AF: 0.287

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.18
Dann	Benign	0.40

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

Other links and lift over

dbSNP: rs724220; hg19: chr1-201630461;