rs1149517
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_014399.4(TSPAN13):c.63+7157A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0147 in 152,328 control chromosomes in the GnomAD database, including 62 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 0.015 ( 62 hom., cov: 32)
Consequence
TSPAN13
NM_014399.4 intron
NM_014399.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.960
Genes affected
TSPAN13 (HGNC:21643): (tetraspanin 13) 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 made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0147 (2233/152328) while in subpopulation AFR AF= 0.0514 (2138/41564). AF 95% confidence interval is 0.0496. There are 62 homozygotes in gnomad4. There are 1052 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 62 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSPAN13 | NM_014399.4 | c.63+7157A>G | intron_variant | ENST00000262067.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSPAN13 | ENST00000262067.5 | c.63+7157A>G | intron_variant | 1 | NM_014399.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0147 AC: 2236AN: 152210Hom.: 62 Cov.: 32
GnomAD3 genomes
?
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0147 AC: 2233AN: 152328Hom.: 62 Cov.: 32 AF XY: 0.0141 AC XY: 1052AN XY: 74494
GnomAD4 genome
?
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2233
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152328
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32
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1052
AN XY:
74494
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5
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at