12-77760826-C-T

Position:

• chr12-77760826-C-T

Variant summary

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

The ENST00000550042.2(NAV3):​c.73-179493C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 151,902 control chromosomes in the GnomAD database, including 21,476 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 0.52 (21476 hom., cov: 31)
• Consequence: NAV3 ENST00000550042.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402

Genes affected

NAV3 (HGNC:15998): (neuron navigator 3) 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. Multiple alternatively spliced transcript variants for this gene have been described but only one has had its full-length nature determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAV3	XM_017020166.3	c.73-179493C>T		intron_variant			XP_016875655.1
NAV3	XM_017020167.1	c.73-179493C>T		intron_variant			XP_016875656.1
NAV3	XM_047429817.1	c.73-179493C>T		intron_variant			XP_047285773.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAV3	ENST00000550042.2	c.73-179493C>T		intron_variant		5		ENSP00000489639.1

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78858 AN: 151784 Hom.: 21429 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.520 AC: 78975 AN: 151902 Hom.: 21476 Cov.: 31 AF XY: 0.513 AC XY: 38074 AN XY: 74244

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.519

Alfa AF: 0.427 Hom.: 2778

Bravo AF: 0.534

Asia WGS AF: 0.446 AC: 1553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5019250; hg19: chr12-78154606;