12-77760826-C-T

Variant names:

• chr12-77760826-C-T
• rs5019250
• ENST00000550042.2:c.73-179493C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

NAV3 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AR Classification: DEFINITIVE Submitted by: Ambry Genetics
• neurodevelopmental disorder

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics

ENSG00000258066 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NAV3	XM_017020166.3	c.73-179493C>T		intron_variant	Intron 1 of 39		XP_016875655.1
NAV3	XM_017020167.1	c.73-179493C>T		intron_variant	Intron 1 of 38		XP_016875656.1
NAV3	XM_047429817.1	c.73-179493C>T		intron_variant	Intron 1 of 37		XP_047285773.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAV3	ENST00000550042.2	c.73-179493C>T		intron_variant	Intron 2 of 8	5		ENSP00000489639.1
ENSG00000258066	ENST00000763016.1	n.53-22437C>T		intron_variant	Intron 1 of 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

African (AFR) AF: 0.691 AC: 28667 AN: 41466

American (AMR) AF: 0.479 AC: 7309 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1701 AN: 3470

East Asian (EAS) AF: 0.446 AC: 2289 AN: 5132

South Asian (SAS) AF: 0.408 AC: 1963 AN: 4816

European-Finnish (FIN) AF: 0.389 AC: 4093 AN: 10532

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.460 AC: 31242 AN: 67918

Other (OTH) AF: 0.519 AC: 1093 AN: 2108

Alfa AF: 0.456 Hom.: 5809

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
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs5019250; hg19: chr12-78154606;