rs10516434

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.14

Publications

2 publications found
Variant links:
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]

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=-0.98).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TSPAN5NM_005723.4 linkc.82-16436G>A intron_variant Intron 1 of 7 ENST00000305798.8 NP_005714.2 P62079

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TSPAN5ENST00000305798.8 linkc.82-16436G>A intron_variant Intron 1 of 7 1 NM_005723.4 ENSP00000307701.3 P62079

Frequencies

GnomAD3 genomes
AF:
0.211
AC:
32095
AN:
151906
Hom.:
3525
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.230
Gnomad AMI
AF:
0.371
Gnomad AMR
AF:
0.176
Gnomad ASJ
AF:
0.264
Gnomad EAS
AF:
0.0944
Gnomad SAS
AF:
0.246
Gnomad FIN
AF:
0.149
Gnomad MID
AF:
0.218
Gnomad NFE
AF:
0.218
Gnomad OTH
AF:
0.227
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.211
AC:
32117
AN:
152024
Hom.:
3529
Cov.:
33
AF XY:
0.206
AC XY:
15275
AN XY:
74308
show subpopulations
African (AFR)
AF:
0.231
AC:
9549
AN:
41426
American (AMR)
AF:
0.176
AC:
2685
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.264
AC:
915
AN:
3464
East Asian (EAS)
AF:
0.0940
AC:
487
AN:
5180
South Asian (SAS)
AF:
0.245
AC:
1181
AN:
4826
European-Finnish (FIN)
AF:
0.149
AC:
1577
AN:
10558
Middle Eastern (MID)
AF:
0.214
AC:
63
AN:
294
European-Non Finnish (NFE)
AF:
0.218
AC:
14850
AN:
67986
Other (OTH)
AF:
0.225
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

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
340
680
1020
1360
1700
<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:
0.213
Hom.:
575
Bravo
AF:
0.210
Asia WGS
AF:
0.236
AC:
819
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.069
DANN
Benign
0.46
PhyloP100
-3.1
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs10516434; hg19: chr4-99445315; API