GeneBe

1-183312569-T-TAAA

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_015039.4(NMNAT2):​c.86-18779_86-18777dupTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000067 ( 0 hom., cov: 0)

Consequence

NMNAT2
NM_015039.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.407

Publications

0 publications found
Variant links:
Genes affected
NMNAT2 (HGNC:16789): (nicotinamide nucleotide adenylyltransferase 2) This gene product belongs to the nicotinamide mononucleotide adenylyltransferase (NMNAT) enzyme family, members of which catalyze an essential step in NAD (NADP) biosynthetic pathway. Unlike the other human family member, which is localized to the nucleus, and is ubiquitously expressed; this enzyme is cytoplasmic, and is predominantly expressed in the brain. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NMNAT2NM_015039.4 linkc.86-18779_86-18777dupTTT intron_variant Intron 1 of 10 ENST00000287713.7 NP_055854.1 Q9BZQ4-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NMNAT2ENST00000287713.7 linkc.86-18777_86-18776insTTT intron_variant Intron 1 of 10 1 NM_015039.4 ENSP00000287713.6 Q9BZQ4-1
ENSG00000305666ENST00000812288.1 linkn.94+501_94+502insAAA intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
AF:
0.00000671
AC:
1
AN:
149110
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000194
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.00000670
AC:
1
AN:
149204
Hom.:
0
Cov.:
0
AF XY:
0.0000138
AC XY:
1
AN XY:
72668
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
0.00
AC:
0
AN:
40710
American (AMR)
AF:
0.00
AC:
0
AN:
15042
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3440
East Asian (EAS)
AF:
0.000194
AC:
1
AN:
5144
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4706
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
9746
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
288
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67168
Other (OTH)
AF:
0.00
AC:
0
AN:
2052
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.225
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.41

Splicing

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

Publications

Other links and lift over

dbSNP: rs5779167; hg19: chr1-183281704; API