rs10488631
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012470.4(TNPO3):c.*1288A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0902 in 152,324 control chromosomes in the GnomAD database, including 860 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 0.090 ( 860 hom., cov: 33)
Exomes 𝑓: 0.33 ( 0 hom. )
Consequence
TNPO3
NM_012470.4 downstream_gene
NM_012470.4 downstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.436
Genes affected
TNPO3 (HGNC:17103): (transportin 3) The protein encoded by this gene is a nuclear import receptor for serine/arginine-rich (SR) proteins such as the splicing factors SFRS1 and SFRS2. The encoded protein has also been shown to be involved in HIV-1 infection, apparently through interaction with the HIV-1 capsid protein. Several protein-coding and non-coding transcript variants have been found for this gene. [provided by RefSeq, Apr 2020]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNPO3 | NM_012470.4 | c.*1288A>G | downstream_gene_variant | ENST00000265388.10 | NP_036602.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0903 AC: 13741AN: 152200Hom.: 863 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
13741
AN:
152200
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.333 AC: 2AN: 6Hom.: 0 AF XY: 0.333 AC XY: 2AN XY: 6 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
6
Hom.:
AF XY:
AC XY:
2
AN XY:
6
Gnomad4 AFR exome
AC:
0
AN:
0
Gnomad4 AMR exome
AC:
0
AN:
0
Gnomad4 ASJ exome
AC:
0
AN:
0
Gnomad4 EAS exome
AC:
0
AN:
0
Gnomad4 SAS exome
AC:
0
AN:
0
Gnomad4 FIN exome
AF:
AC:
0
AN:
2
Gnomad4 NFE exome
AF:
AC:
2
AN:
4
Gnomad4 Remaining exome
AC:
0
AN:
0
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0902 AC: 13736AN: 152318Hom.: 860 Cov.: 33 AF XY: 0.0929 AC XY: 6918AN XY: 74484 show subpopulations
GnomAD4 genome
AF:
AC:
13736
AN:
152318
Hom.:
Cov.:
33
AF XY:
AC XY:
6918
AN XY:
74484
Gnomad4 AFR
AF:
AC:
0.0243662
AN:
0.0243662
Gnomad4 AMR
AF:
AC:
0.137724
AN:
0.137724
Gnomad4 ASJ
AF:
AC:
0.114187
AN:
0.114187
Gnomad4 EAS
AF:
AC:
0.00192678
AN:
0.00192678
Gnomad4 SAS
AF:
AC:
0.153002
AN:
0.153002
Gnomad4 FIN
AF:
AC:
0.144863
AN:
0.144863
Gnomad4 NFE
AF:
AC:
0.112457
AN:
0.112457
Gnomad4 OTH
AF:
AC:
0.101044
AN:
0.101044
Heterozygous variant carriers
0
625
1250
1876
2501
3126
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
172
344
516
688
860
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
204
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at