rs16838134
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001316349.2(THSD7B):c.1369+5724T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0139 in 152,234 control chromosomes in the GnomAD database, including 60 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 0.014 ( 60 hom., cov: 33)
Consequence
THSD7B
NM_001316349.2 intron
NM_001316349.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.265
Genes affected
THSD7B (HGNC:29348): (thrombospondin type 1 domain containing 7B) Predicted to be involved in actin cytoskeleton reorganization. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.82).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0139 (2115/152234) while in subpopulation AFR AF= 0.0481 (1996/41532). AF 95% confidence interval is 0.0463. There are 60 homozygotes in gnomad4. There are 977 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 60 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THSD7B | NM_001316349.2 | c.1369+5724T>C | intron_variant | ENST00000409968.6 | |||
THSD7B | XM_047445935.1 | c.946+5724T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THSD7B | ENST00000409968.6 | c.1369+5724T>C | intron_variant | 5 | NM_001316349.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0139 AC: 2109AN: 152116Hom.: 60 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0139 AC: 2115AN: 152234Hom.: 60 Cov.: 33 AF XY: 0.0131 AC XY: 977AN XY: 74442
GnomAD4 genome
?
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2115
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33
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977
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74442
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3476
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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