11-19519590-A-T

Variant names:

• chr11-19519590-A-T
• rs1487181
• ENST00000360655.8:c.75+168563A>T

Variant summary

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

The NM_001111018.2(NAV2):​c.75+168563A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,004 control chromosomes in the GnomAD database, including 13,620 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 0.42 (13620 hom., cov: 32)
• Consequence: NAV2 NM_001111018.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.931
• Publications: 2 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]

NAV2-AS4 (HGNC:40741): (NAV2 antisense RNA 4)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001111018.2. 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_001111018.2		c.75+168563A>T		intron	N/A	NP_001104488.1	Q8IVL1-4
	NAV2-AS4	NR_033989.1		n.338+160T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAV2	ENST00000360655.8	TSL:1	c.75+168563A>T		intron	N/A	ENSP00000353871.4	Q8IVL1-4
	NAV2-AS4	ENST00000532874.1	TSL:5	n.147+160T>A		intron	N/A
	NAV2-AS4	ENST00000837121.1		n.343+160T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63219 AN: 151886 Hom.: 13603 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.416 AC: 63280 AN: 152004 Hom.: 13620 Cov.: 32 AF XY: 0.413 AC XY: 30656 AN XY: 74298

African (AFR) AF: 0.506 AC: 20947 AN: 41434

American (AMR) AF: 0.462 AC: 7065 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1591 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2039 AN: 5146

South Asian (SAS) AF: 0.379 AC: 1823 AN: 4812

European-Finnish (FIN) AF: 0.290 AC: 3067 AN: 10582

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.372 AC: 25298 AN: 67964

Other (OTH) AF: 0.437 AC: 922 AN: 2112

Alfa AF: 0.393 Hom.: 1531

Bravo AF: 0.436

Asia WGS AF: 0.379 AC: 1319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.80
DANN	Benign	0.69
PhyloP100		-0.93
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1487181; hg19: chr11-19541137;