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GeneBe

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 151804 control chromosomes in the gnomAD Genomes database, including 42921 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 ( 42921 hom., cov: 32)

Consequence

TSPAN8
ENST00000393330.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.93

Links

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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
?
GnomAd 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
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
0.0020
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