chr11-19548016-C-A

Variant names:

• chr11-19548016-C-A
• rs874426
• ENST00000360655.8:c.75+196989C>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+196989C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,064 control chromosomes in the GnomAD database, including 39,597 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 0.70 (39597 hom., cov: 32)
• Consequence: NAV2 ENST00000360655.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 15 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAV2	NM_001111018.2	c.75+196989C>A		intron_variant	Intron 2 of 38		NP_001104488.1
NAV2	XM_017018520.3	c.75+196989C>A		intron_variant	Intron 2 of 41		XP_016874009.1
NAV2	XM_024448758.2	c.75+196989C>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+196989C>A		intron_variant	Intron 1 of 37	1		ENSP00000353871.4

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106541 AN: 151946 Hom.: 39601 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.701 AC: 106578 AN: 152064 Hom.: 39597 Cov.: 32 AF XY: 0.702 AC XY: 52188 AN XY: 74322

African (AFR) AF: 0.453 AC: 18771 AN: 41458

American (AMR) AF: 0.745 AC: 11383 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2712 AN: 3466

East Asian (EAS) AF: 0.448 AC: 2313 AN: 5160

South Asian (SAS) AF: 0.745 AC: 3588 AN: 4816

European-Finnish (FIN) AF: 0.829 AC: 8773 AN: 10586

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56422 AN: 67976

Other (OTH) AF: 0.717 AC: 1513 AN: 2110

Alfa AF: 0.780 Hom.: 205226

Bravo AF: 0.679

Asia WGS AF: 0.567 AC: 1973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.082
DANN	Benign	0.61
PhyloP100		-1.3
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: rs874426; hg19: chr11-19569563;