NM_145117.5:c.932-8870A>C

Variant names:

• chr11-19924306-A-C
• rs10444227
• NM_145117.5:c.932-8870A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145117.5(NAV2):​c.932-8870A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,362 control chromosomes in the GnomAD database, including 12,158 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 0.36 (12158 hom., cov: 31)
• Consequence: NAV2 NM_145117.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145117.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAV2	NM_145117.5	MANE Select	c.932-8870A>C		intron	N/A	NP_660093.2
	NAV2	NM_001244963.2		c.1001-8870A>C		intron	N/A	NP_001231892.1
	NAV2	NM_182964.6		c.932-8870A>C		intron	N/A	NP_892009.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAV2	ENST00000349880.9	TSL:1 MANE Select	c.932-8870A>C		intron	N/A	ENSP00000309577.6
	NAV2	ENST00000360655.8	TSL:1	c.740-8870A>C		intron	N/A	ENSP00000353871.4
	NAV2	ENST00000396087.7	TSL:5	c.1001-8870A>C		intron	N/A	ENSP00000379396.3

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54709 AN: 151250 Hom.: 12159 Cov.: 31

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.372

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.361 AC: 54709 AN: 151362 Hom.: 12158 Cov.: 31 AF XY: 0.361 AC XY: 26683 AN XY: 73944

African (AFR) AF: 0.111 AC: 4591 AN: 41442

American (AMR) AF: 0.312 AC: 4753 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1497 AN: 3470

East Asian (EAS) AF: 0.285 AC: 1472 AN: 5160

South Asian (SAS) AF: 0.375 AC: 1802 AN: 4806

European-Finnish (FIN) AF: 0.505 AC: 5169 AN: 10226

Middle Eastern (MID) AF: 0.364 AC: 102 AN: 280

European-Non Finnish (NFE) AF: 0.503 AC: 34065 AN: 67746

Other (OTH) AF: 0.379 AC: 798 AN: 2106

Alfa AF: 0.429 Hom.: 4997

Bravo AF: 0.333

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.44
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10444227; hg19: chr11-19945852;