11-19746068-A-G

Variant names:

• chr11-19746068-A-G
• rs4757841
• NM_145117.5:c.267+32106A>G

Variant summary

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

The NM_145117.5(NAV2):​c.267+32106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 152,162 control chromosomes in the GnomAD database, including 13,706 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 0.39 (13706 hom., cov: 33)
• Consequence: NAV2 NM_145117.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.585 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAV2	NM_145117.5	MANE Select	c.267+32106A>G		intron	N/A	NP_660093.2
	NAV2	NM_001244963.2		c.267+32106A>G		intron	N/A	NP_001231892.1	Q8IVL1-1
	NAV2	NM_182964.6		c.267+32106A>G		intron	N/A	NP_892009.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAV2	ENST00000349880.9	TSL:1 MANE Select	c.267+32106A>G		intron	N/A	ENSP00000309577.6	Q8IVL1-3
	NAV2	ENST00000360655.8	TSL:1	c.76-86416A>G		intron	N/A	ENSP00000353871.4	Q8IVL1-4
	NAV2	ENST00000396087.7	TSL:5	c.267+32106A>G		intron	N/A	ENSP00000379396.3	Q8IVL1-1

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59812 AN: 152044 Hom.: 13698 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.393 AC: 59833 AN: 152162 Hom.: 13706 Cov.: 33 AF XY: 0.399 AC XY: 29657 AN XY: 74382

African (AFR) AF: 0.153 AC: 6340 AN: 41534

American (AMR) AF: 0.555 AC: 8475 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1565 AN: 3472

East Asian (EAS) AF: 0.603 AC: 3117 AN: 5172

South Asian (SAS) AF: 0.307 AC: 1480 AN: 4818

European-Finnish (FIN) AF: 0.501 AC: 5297 AN: 10574

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32124 AN: 67992

Other (OTH) AF: 0.410 AC: 867 AN: 2114

Alfa AF: 0.445 Hom.: 8762

Bravo AF: 0.393

Asia WGS AF: 0.434 AC: 1508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.1
DANN	Benign	0.75
PhyloP100		1.0
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: rs4757841; hg19: chr11-19767614;