rs726217
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001008693.3(CST9):c.*31C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 1,608,140 control chromosomes in the GnomAD database, including 282,424 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 0.49 ( 21513 hom., cov: 32)
Exomes 𝑓: 0.59 ( 260911 hom. )
Consequence
CST9
NM_001008693.3 3_prime_UTR
NM_001008693.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.435
Genes affected
CST9 (HGNC:13261): (cystatin 9) The cystatin superfamily encompasses proteins that contain multiple cystatin-like sequences. Some of the members are active cysteine protease inhibitors, while others have lost or perhaps never acquired this inhibitory activity. There are three inhibitory families in the superfamily, including the type 1 cystatins (stefins), type 2 cystatins and the kininogens. The type 2 cystatin proteins are a class of cysteine proteinase inhibitors found in a variety of human fluids and secretions, where they appear to provide protective functions. The cystatin locus on chromosome 20 contains the majority of the type 2 cystatin genes and pseudogenes. This gene is located in the cystatin locus and encodes a secreted protein that may play a role in hematopoietic differentiation or inflammation. [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=-0.89).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CST9 | NM_001008693.3 | c.*31C>T | 3_prime_UTR_variant | 2/2 | ENST00000376971.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CST9 | ENST00000376971.4 | c.*31C>T | 3_prime_UTR_variant | 2/2 | 1 | NM_001008693.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.494 AC: 75042AN: 151870Hom.: 21509 Cov.: 32
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GnomAD3 exomes AF: 0.585 AC: 140693AN: 240430Hom.: 42723 AF XY: 0.588 AC XY: 76354AN XY: 129824
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GnomAD4 exome AF: 0.594 AC: 864270AN: 1456152Hom.: 260911 Cov.: 52 AF XY: 0.592 AC XY: 428782AN XY: 723798
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GnomAD4 genome ? AF: 0.494 AC: 75054AN: 151988Hom.: 21513 Cov.: 32 AF XY: 0.501 AC XY: 37221AN XY: 74290
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ClinVar
Not reported inComputational scores
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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