11-19683686-C-T

Variant names:

• chr11-19683686-C-T
• rs12295525
• ENST00000360655.8:c.76-148798C>T

Variant summary

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

The ENST00000360655.8(NAV2):​c.76-148798C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,206 control chromosomes in the GnomAD database, including 1,114 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 0.11 (1114 hom., cov: 33)
• Consequence: NAV2 ENST00000360655.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAV2	NM_001111018.2	c.76-148798C>T		intron_variant	Intron 2 of 38		NP_001104488.1
NAV2	XM_017018520.3	c.76-148798C>T		intron_variant	Intron 2 of 41		XP_016874009.1
NAV2	XM_024448758.2	c.76-148798C>T		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.76-148798C>T		intron_variant	Intron 1 of 37	1		ENSP00000353871.4

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16767 AN: 152088 Hom.: 1114 Cov.: 33

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0734

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0640

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0910

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.110 AC: 16783 AN: 152206 Hom.: 1114 Cov.: 33 AF XY: 0.107 AC XY: 7960 AN XY: 74418

African (AFR) AF: 0.173 AC: 7204 AN: 41526

American (AMR) AF: 0.0732 AC: 1120 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 537 AN: 3470

East Asian (EAS) AF: 0.00386 AC: 20 AN: 5176

South Asian (SAS) AF: 0.148 AC: 713 AN: 4828

European-Finnish (FIN) AF: 0.0640 AC: 678 AN: 10590

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0910 AC: 6188 AN: 68002

Other (OTH) AF: 0.103 AC: 217 AN: 2114

Alfa AF: 0.0593 Hom.: 89

Bravo AF: 0.112

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.34
PhyloP100		0.042
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: rs12295525; hg19: chr11-19705232;