rs10488631

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.436
Variant links:
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]

Genome browser will be placed here

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
TNPO3NM_012470.4 linkc.*1288A>G downstream_gene_variant ENST00000265388.10 NP_036602.1 Q9Y5L0-2A0A024R794B3KMX1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TNPO3ENST00000265388.10 linkc.*1288A>G downstream_gene_variant 1 NM_012470.4 ENSP00000265388.5 Q9Y5L0-2
TNPO3ENST00000627585.2 linkc.*1288A>G downstream_gene_variant 2 ENSP00000487231.1 C9J7E5

Frequencies

GnomAD3 genomes
AF:
0.0903
AC:
13741
AN:
152200
Hom.:
863
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0244
Gnomad AMI
AF:
0.0373
Gnomad AMR
AF:
0.138
Gnomad ASJ
AF:
0.114
Gnomad EAS
AF:
0.00192
Gnomad SAS
AF:
0.153
Gnomad FIN
AF:
0.145
Gnomad MID
AF:
0.130
Gnomad NFE
AF:
0.112
Gnomad OTH
AF:
0.102
GnomAD4 exome
AF:
0.333
AC:
2
AN:
6
Hom.:
0
AF XY:
0.333
AC XY:
2
AN XY:
6
show subpopulations
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:
0.00
AC:
0
AN:
2
Gnomad4 NFE exome
AF:
0.500
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:
13736
AN:
152318
Hom.:
860
Cov.:
33
AF XY:
0.0929
AC XY:
6918
AN XY:
74484
show subpopulations
Gnomad4 AFR
AF:
0.0244
AC:
0.0243662
AN:
0.0243662
Gnomad4 AMR
AF:
0.138
AC:
0.137724
AN:
0.137724
Gnomad4 ASJ
AF:
0.114
AC:
0.114187
AN:
0.114187
Gnomad4 EAS
AF:
0.00193
AC:
0.00192678
AN:
0.00192678
Gnomad4 SAS
AF:
0.153
AC:
0.153002
AN:
0.153002
Gnomad4 FIN
AF:
0.145
AC:
0.144863
AN:
0.144863
Gnomad4 NFE
AF:
0.112
AC:
0.112457
AN:
0.112457
Gnomad4 OTH
AF:
0.101
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:
0.104
Hom.:
4099
Bravo
AF:
0.0868
Asia WGS
AF:
0.0590
AC:
204
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
5.8
DANN
Benign
0.65

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: rs10488631; hg19: chr7-128594183; API