chr11-19731153-T-G

Variant names:

• chr11-19731153-T-G
• rs2042600
• NM_145117.5:c.267+17191T>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+17191T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,112 control chromosomes in the GnomAD database, including 29,526 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 0.60 (29526 hom., cov: 33)
• Consequence: NAV2 NM_145117.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAV2	NM_145117.5	c.267+17191T>G		intron_variant	Intron 1 of 37	ENST00000349880.9	NP_660093.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAV2	ENST00000349880.9	c.267+17191T>G		intron_variant	Intron 1 of 37	1	NM_145117.5	ENSP00000309577.6
NAV2	ENST00000360655.8	c.76-101331T>G		intron_variant	Intron 1 of 37	1		ENSP00000353871.4
NAV2	ENST00000396087.7	c.267+17191T>G		intron_variant	Intron 1 of 40	5		ENSP00000379396.3
NAV2	ENST00000396085.6	c.267+17191T>G		intron_variant	Intron 1 of 38	5		ENSP00000379394.1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91665 AN: 151994 Hom.: 29466 Cov.: 33

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.603 AC: 91782 AN: 152112 Hom.: 29526 Cov.: 33 AF XY: 0.599 AC XY: 44537 AN XY: 74366

African (AFR) AF: 0.842 AC: 34959 AN: 41514

American (AMR) AF: 0.475 AC: 7273 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2066 AN: 3472

East Asian (EAS) AF: 0.407 AC: 2101 AN: 5162

South Asian (SAS) AF: 0.565 AC: 2724 AN: 4818

European-Finnish (FIN) AF: 0.526 AC: 5562 AN: 10582

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35297 AN: 67956

Other (OTH) AF: 0.585 AC: 1233 AN: 2108

Alfa AF: 0.547 Hom.: 16813

Bravo AF: 0.605

Asia WGS AF: 0.504 AC: 1753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.85
PhyloP100		-0.71
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: rs2042600; hg19: chr11-19752699;