rs2028608

Variant names:

• chr11-19906798-G-A
• rs2028608
• NM_145117.5:c.931+14204G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-19906798-G-A
• chr11-19906798-G-C
• chr11-19906798-G-T

Variant summary

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

The NM_145117.5(NAV2):​c.931+14204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 151,956 control chromosomes in the GnomAD database, including 27,270 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 0.58 (27270 hom., cov: 31)
• Consequence: NAV2 NM_145117.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.689
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAV2	NM_145117.5	c.931+14204G>A		intron_variant	Intron 6 of 37	ENST00000349880.9	NP_660093.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAV2	ENST00000349880.9	c.931+14204G>A		intron_variant	Intron 6 of 37	1	NM_145117.5	ENSP00000309577.6
NAV2	ENST00000360655.8	c.739+14204G>A		intron_variant	Intron 6 of 37	1		ENSP00000353871.4
NAV2	ENST00000396087.7	c.1000+14204G>A		intron_variant	Intron 7 of 40	5		ENSP00000379396.3
NAV2	ENST00000396085.6	c.931+14204G>A		intron_variant	Intron 6 of 38	5		ENSP00000379394.1

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88776 AN: 151838 Hom.: 27261 Cov.: 31

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.584 AC: 88815 AN: 151956 Hom.: 27270 Cov.: 31 AF XY: 0.594 AC XY: 44132 AN XY: 74256

African (AFR) AF: 0.379 AC: 15697 AN: 41416

American (AMR) AF: 0.646 AC: 9860 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2262 AN: 3470

East Asian (EAS) AF: 0.782 AC: 4013 AN: 5134

South Asian (SAS) AF: 0.695 AC: 3344 AN: 4814

European-Finnish (FIN) AF: 0.759 AC: 8033 AN: 10582

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43654 AN: 67956

Other (OTH) AF: 0.583 AC: 1230 AN: 2108

Alfa AF: 0.622 Hom.: 51102

Bravo AF: 0.566

Asia WGS AF: 0.699 AC: 2428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.5
DANN	Benign	0.61
PhyloP100		0.69
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: rs2028608; hg19: chr11-19928344;