1-201625537-T-C

Variant names:

• chr1-201625537-T-C
• rs2068824
• NM_001389617.1:c.722+1931T>C

Variant summary

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

The NM_001389617.1(NAV1):​c.722+1931T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0691 in 152,274 control chromosomes in the GnomAD database, including 483 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 0.069 (483 hom., cov: 32)
• Consequence: NAV1 NM_001389617.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.849
• Publications: 7 publications found

Genes affected

NAV1 (HGNC:15989): (neuron navigator 1) This gene belongs to the neuron navigator family and is expressed predominantly in the nervous system. The encoded protein contains coiled-coil domains and a conserved AAA domain characteristic for ATPases associated with a variety of cellular activities. This gene is similar to unc-53, a Caenorhabditis elegans gene involved in axon guidance. The exact function of this gene is not known, but it is thought to play a role in in neuronal development and regeneration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2009]

LOC124904482 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NAV1	NM_001389617.1	c.722+1931T>C		intron_variant	Intron 3 of 33	ENST00000685211.1	NP_001376546.1
NAV1	NM_001389616.1	c.722+1931T>C		intron_variant	Intron 2 of 31		NP_001376545.1
NAV1	NM_001389615.1	c.722+1931T>C		intron_variant	Intron 3 of 30		NP_001376544.1
LOC124904482	XR_007066789.1	n.17626+4822A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NAV1	ENST00000685211.1	c.722+1931T>C		intron_variant	Intron 3 of 33		NM_001389617.1	ENSP00000510803.1
NAV1	ENST00000367302.5	c.-101+1931T>C		intron_variant	Intron 1 of 29	5		ENSP00000356271.1
NAV1	ENST00000850636.1	c.722+1931T>C		intron_variant	Intron 3 of 6			ENSP00000520915.1
NAV1	ENST00000491403.1	n.324+1931T>C		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0691 AC: 10518 AN: 152156 Hom.: 484 Cov.: 32

Gnomad AFR AF: 0.0778

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.0508

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.0335

Gnomad FIN AF: 0.0491

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0624

Gnomad OTH AF: 0.0573

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

GnomAD4 genome AF: 0.0691 AC: 10515 AN: 152274 Hom.: 483 Cov.: 32 AF XY: 0.0681 AC XY: 5073 AN XY: 74456

African (AFR) AF: 0.0777 AC: 3229 AN: 41550

American (AMR) AF: 0.0507 AC: 776 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0112 AC: 39 AN: 3472

East Asian (EAS) AF: 0.267 AC: 1378 AN: 5162

South Asian (SAS) AF: 0.0334 AC: 161 AN: 4826

European-Finnish (FIN) AF: 0.0491 AC: 521 AN: 10618

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0624 AC: 4243 AN: 68022

Other (OTH) AF: 0.0558 AC: 118 AN: 2116

Alfa AF: 0.0617 Hom.: 525

Bravo AF: 0.0715

Asia WGS AF: 0.136 AC: 474 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	0.16
DANN	Benign	0.41
PhyloP100		-0.85
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: rs2068824; hg19: chr1-201594665;