chr1-201777111-G-T

Position:

• chr1-201777111-G-T

Variant summary

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

The NM_001389617.1(NAV1):​c.2088-3310G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0715 in 152,292 control chromosomes in the GnomAD database, including 789 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 0.072 (789 hom., cov: 32)
• Consequence: NAV1 NM_001389617.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

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]

LOC124904483 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAV1	NM_001389617.1	c.2088-3310G>T		intron_variant		ENST00000685211.1	NP_001376546.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAV1	ENST00000685211.1	c.2088-3310G>T		intron_variant			NM_001389617.1	ENSP00000510803.1

Frequencies

GnomAD3 genomes AF: 0.0715 AC: 10878 AN: 152174 Hom.: 784 Cov.: 32

Gnomad AFR AF: 0.0153

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0425

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0605

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0715 AC: 10890 AN: 152292 Hom.: 789 Cov.: 32 AF XY: 0.0775 AC XY: 5772 AN XY: 74464

Gnomad4 AFR AF: 0.0153

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0425

Gnomad4 NFE AF: 0.0605

Gnomad4 OTH AF: 0.0709

Alfa AF: 0.0707 Hom.: 806

Bravo AF: 0.0812

Asia WGS AF: 0.197 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.75
DANN	Benign	0.64

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: rs523218; hg19: chr1-201746239;