rs1527047

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_007063383.1(LOC124902972):​n.1516A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 151,934 control chromosomes in the GnomAD database, including 24,927 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 0.57 ( 24927 hom., cov: 31)
Exomes 𝑓: 0.43 ( 0 hom. )

Consequence

LOC124902972
XR_007063383.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.678
Variant links:
Genes affected
NAV3 (HGNC:15998): (neuron navigator 3) 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. Multiple alternatively spliced transcript variants for this gene have been described but only one has had its full-length nature determined. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC124902972XR_007063383.1 linkuse as main transcriptn.1516A>G non_coding_transcript_exon_variant 1/2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NAV3ENST00000550042.2 linkuse as main transcriptc.-337+54555A>G intron_variant 5
ENST00000552736.2 linkuse as main transcript upstream_gene_variant 3

Frequencies

GnomAD3 genomes
AF:
0.569
AC:
86337
AN:
151802
Hom.:
24931
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.527
Gnomad AMI
AF:
0.590
Gnomad AMR
AF:
0.547
Gnomad ASJ
AF:
0.549
Gnomad EAS
AF:
0.462
Gnomad SAS
AF:
0.396
Gnomad FIN
AF:
0.556
Gnomad MID
AF:
0.573
Gnomad NFE
AF:
0.621
Gnomad OTH
AF:
0.589
GnomAD4 exome
AF:
0.429
AC:
6
AN:
14
Hom.:
0
AF XY:
0.500
AC XY:
3
AN XY:
6
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.500
Gnomad4 NFE exome
AF:
0.500
Gnomad4 OTH exome
AF:
0.500
GnomAD4 genome
AF:
0.568
AC:
86354
AN:
151920
Hom.:
24927
Cov.:
31
AF XY:
0.561
AC XY:
41679
AN XY:
74244
show subpopulations
Gnomad4 AFR
AF:
0.527
Gnomad4 AMR
AF:
0.546
Gnomad4 ASJ
AF:
0.549
Gnomad4 EAS
AF:
0.462
Gnomad4 SAS
AF:
0.395
Gnomad4 FIN
AF:
0.556
Gnomad4 NFE
AF:
0.621
Gnomad4 OTH
AF:
0.584
Alfa
AF:
0.600
Hom.:
12650
Bravo
AF:
0.570
Asia WGS
AF:
0.456
AC:
1587
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.42
DANN
Benign
0.73

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1527047; hg19: chr12-77773549; API