rs10516434
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005723.4(TSPAN5):c.82-16436G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,024 control chromosomes in the GnomAD database, including 3,529 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 0.21 ( 3529 hom., cov: 33)
Consequence
TSPAN5
NM_005723.4 intron
NM_005723.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.14
Publications
2 publications found
Genes affected
TSPAN5 (HGNC:17753): (tetraspanin 5) The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. [provided by RefSeq, Jul 2008]
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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=-0.98).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.211 AC: 32095AN: 151906Hom.: 3525 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
32095
AN:
151906
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.211 AC: 32117AN: 152024Hom.: 3529 Cov.: 33 AF XY: 0.206 AC XY: 15275AN XY: 74308 show subpopulations
GnomAD4 genome
AF:
AC:
32117
AN:
152024
Hom.:
Cov.:
33
AF XY:
AC XY:
15275
AN XY:
74308
show subpopulations
African (AFR)
AF:
AC:
9549
AN:
41426
American (AMR)
AF:
AC:
2685
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
AC:
915
AN:
3464
East Asian (EAS)
AF:
AC:
487
AN:
5180
South Asian (SAS)
AF:
AC:
1181
AN:
4826
European-Finnish (FIN)
AF:
AC:
1577
AN:
10558
Middle Eastern (MID)
AF:
AC:
63
AN:
294
European-Non Finnish (NFE)
AF:
AC:
14850
AN:
67986
Other (OTH)
AF:
AC:
472
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1304
2608
3911
5215
6519
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
819
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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