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rs7961581

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000393330.6(TSPAN8):c.-110+8029G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 151,922 control chromosomes in the GnomAD database, including 42,953 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 0.75 ( 42953 hom., cov: 32)

Consequence

TSPAN8
ENST00000393330.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.93
Variant links:
Genes affected
TSPAN8 (HGNC:11855): (tetraspanin 8) 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. This encoded protein is a cell surface glycoprotein that is known to complex with integrins. This gene is expressed in different carcinomas. The use of alternate polyadenylation sites has been found for this gene. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TSPAN8ENST00000393330.6 linkuse as main transcriptc.-110+8029G>A intron_variant 1 P1
TSPAN8ENST00000549421.1 linkuse as main transcriptn.206+13394G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.750
AC:
113857
AN:
151804
Hom.:
42921
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.796
Gnomad AMI
AF:
0.747
Gnomad AMR
AF:
0.777
Gnomad ASJ
AF:
0.679
Gnomad EAS
AF:
0.777
Gnomad SAS
AF:
0.669
Gnomad FIN
AF:
0.793
Gnomad MID
AF:
0.661
Gnomad NFE
AF:
0.718
Gnomad OTH
AF:
0.712
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.750
AC:
113950
AN:
151922
Hom.:
42953
Cov.:
32
AF XY:
0.751
AC XY:
55762
AN XY:
74218
show subpopulations
Gnomad4 AFR
AF:
0.796
Gnomad4 AMR
AF:
0.778
Gnomad4 ASJ
AF:
0.679
Gnomad4 EAS
AF:
0.776
Gnomad4 SAS
AF:
0.669
Gnomad4 FIN
AF:
0.793
Gnomad4 NFE
AF:
0.718
Gnomad4 OTH
AF:
0.711
Alfa
AF:
0.721
Hom.:
73610
Bravo
AF:
0.754
Asia WGS
AF:
0.744
AC:
2584
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
Cadd
Benign
0.021
Dann
Benign
0.71

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs7961581; hg19: chr12-71663102; API