rs9806183
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_024817.3(THSD4):c.1015+25745G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00404 in 145,038 control chromosomes in the GnomAD database, including 3 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 0.0040 ( 3 hom., cov: 31)
Consequence
THSD4
NM_024817.3 intron
NM_024817.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.129
Genes affected
THSD4 (HGNC:25835): (thrombospondin type 1 domain containing 4) Predicted to enable hydrolase activity. Predicted to be an extracellular matrix structural constituent. Predicted to act upstream of or within elastic fiber assembly. Located in collagen-containing extracellular matrix and extracellular exosome. [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=-0.9).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00404 (586/145038) while in subpopulation AFR AF= 0.0148 (564/38074). AF 95% confidence interval is 0.0138. There are 3 homozygotes in gnomad4. There are 263 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 582 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THSD4 | NM_024817.3 | c.1015+25745G>A | intron_variant | ENST00000261862.8 | |||
LOC124903521 | XR_007064701.1 | n.6337G>A | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THSD4 | ENST00000261862.8 | c.1015+25745G>A | intron_variant | 5 | NM_024817.3 | P1 | |||
THSD4 | ENST00000355327.7 | c.1015+25745G>A | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00402 AC: 582AN: 144912Hom.: 3 Cov.: 31
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00404 AC: 586AN: 145038Hom.: 3 Cov.: 31 AF XY: 0.00372 AC XY: 263AN XY: 70636
GnomAD4 genome
?
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70636
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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