chr11-19391114-G-A

Variant names:

• chr11-19391114-G-A
• rs4073508
• ENST00000360655.8:c.75+40087G>A

Variant summary

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

The ENST00000360655.8(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 ENST00000360655.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• 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]

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 (AMR) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAV2	NM_001111018.2	c.75+40087G>A		intron_variant	Intron 2 of 38		NP_001104488.1
NAV2	XM_017018520.3	c.75+40087G>A		intron_variant	Intron 2 of 41		XP_016874009.1
NAV2	XM_024448758.2	c.75+40087G>A		intron_variant	Intron 1 of 40		XP_024304526.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAV2	ENST00000360655.8	c.75+40087G>A		intron_variant	Intron 1 of 37	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

African (AFR) AF: 0.331 AC: 13677 AN: 41382

American (AMR) AF: 0.749 AC: 11456 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2682 AN: 3468

East Asian (EAS) AF: 0.543 AC: 2807 AN: 5166

South Asian (SAS) AF: 0.648 AC: 3109 AN: 4800

European-Finnish (FIN) AF: 0.794 AC: 8393 AN: 10570

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.722 AC: 49044 AN: 67942

Other (OTH) AF: 0.659 AC: 1391 AN: 2110

Alfa AF: 0.688 Hom.: 142038

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
PhyloP100		-0.70
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: rs4073508; hg19: chr11-19412661;