rs9350504
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_133493.5(CD109):c.634-8536T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0738 in 152,166 control chromosomes in the GnomAD database, including 870 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 0.074 ( 870 hom., cov: 31)
Consequence
CD109
NM_133493.5 intron
NM_133493.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.07
Genes affected
CD109 (HGNC:21685): (CD109 molecule) This gene encodes a glycosyl phosphatidylinositol (GPI)-linked glycoprotein that localizes to the surface of platelets, activated T-cells, and endothelial cells. The protein binds to and negatively regulates signalling by transforming growth factor beta (TGF-beta). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2014]
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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=-1.04).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD109 | NM_133493.5 | c.634-8536T>C | intron_variant | ENST00000287097.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD109 | ENST00000287097.6 | c.634-8536T>C | intron_variant | 1 | NM_133493.5 | P1 | |||
CD109 | ENST00000422508.6 | c.403-8536T>C | intron_variant | 1 | |||||
CD109 | ENST00000437994.6 | c.634-8536T>C | intron_variant | 1 | |||||
CD109 | ENST00000649530.1 | n.606-8536T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0736 AC: 11188AN: 152046Hom.: 856 Cov.: 31
GnomAD3 genomes
?
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11188
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152046
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0738 AC: 11228AN: 152166Hom.: 870 Cov.: 31 AF XY: 0.0777 AC XY: 5781AN XY: 74406
GnomAD4 genome
?
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11228
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152166
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31
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5781
AN XY:
74406
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Asia WGS
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905
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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