rs2028608

chr11-19906798-G-Achr11-19906798-G-Cchr11-19906798-G-T

Variant summary

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

The NM_145117.5(NAV2):c.931+14204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 151,956 control chromosomes in the GnomAD database, including 27,270 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 0.58 (27270 hom., cov: 31)
• Consequence: NAV2 NM_145117.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.689

Genes affected

NAV2 (HGNC:15997): (neuron navigator 2) This gene encodes a member of the neuron navigator gene family, which may play a role in cellular growth and migration. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NAV2	NM_145117.5	c.931+14204G>A		intron_variant		ENST00000349880.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAV2	ENST00000349880.9	c.931+14204G>A		intron_variant		1	NM_145117.5
NAV2	ENST00000360655.8	c.739+14204G>A		intron_variant		1		P1
NAV2	ENST00000396085.6	c.931+14204G>A		intron_variant		5
NAV2	ENST00000396087.7	c.1000+14204G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88776 AN: 151838 Hom.: 27261 Cov.: 31

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.584 AC: 88815 AN: 151956 Hom.: 27270 Cov.: 31 AF XY: 0.594 AC XY: 44132 AN XY: 74256

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.782

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.583

Alfa AF: 0.629 Hom.: 41279

Bravo AF: 0.566

Asia WGS AF: 0.699 AC: 2428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.5
Dann	Benign	0.61

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: rs2028608; hg19: chr11-19928344;