rs4073508

Positions:

• chr11-19391114-G-A

Variant summary

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

The NM_001111018.2(NAV2):​c.75+40087G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 151,928 control chromosomes in the GnomAD database, including 31,025 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 0.61 (31025 hom., cov: 30)
• Consequence: NAV2 NM_001111018.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAV2	NM_001111018.2	c.75+40087G>A		intron_variant			NP_001104488.1
NAV2	XM_017018520.3	c.75+40087G>A		intron_variant			XP_016874009.1
NAV2	XM_024448758.2	c.75+40087G>A		intron_variant			XP_024304526.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAV2	ENST00000360655.8	c.75+40087G>A		intron_variant		1		ENSP00000353871.4

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93187 AN: 151810 Hom.: 31009 Cov.: 30

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.614 AC: 93227 AN: 151928 Hom.: 31025 Cov.: 30 AF XY: 0.622 AC XY: 46178 AN XY: 74274

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.794

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.659

Alfa AF: 0.708 Hom.: 63637

Bravo AF: 0.598

Asia WGS AF: 0.592 AC: 2062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.45
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4073508; hg19: chr11-19412661;