11-19610593-C-T

Position:

• chr11-19610593-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001111018.2(NAV2):​c.76-221891C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 152,168 control chromosomes in the GnomAD database, including 50,127 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 0.76 (50127 hom., cov: 33)
• Consequence: NAV2 NM_001111018.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NAV2	NM_001111018.2	c.76-221891C>T		intron_variant			NP_001104488.1
NAV2	XM_017018520.3	c.76-221891C>T		intron_variant			XP_016874009.1
NAV2	XM_024448758.2	c.76-221891C>T		intron_variant			XP_024304526.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAV2	ENST00000360655.8	c.76-221891C>T		intron_variant		1		ENSP00000353871.4

Frequencies

GnomAD3 genomes AF: 0.764 AC: 116218 AN: 152050 Hom.: 50125 Cov.: 33

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.905

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.764 AC: 116223 AN: 152168 Hom.: 50127 Cov.: 33 AF XY: 0.765 AC XY: 56926 AN XY: 74390

Gnomad4 AFR AF: 0.329

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.924

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.905

Gnomad4 NFE AF: 0.963

Gnomad4 OTH AF: 0.800

Alfa AF: 0.912 Hom.: 36269

Bravo AF: 0.742

Asia WGS AF: 0.750 AC: 2610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.5
DANN	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1487214; hg19: chr11-19632139;