rs36212406
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022034.6(CUZD1):c.233+192C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00107 in 152,238 control chromosomes in the GnomAD database, including 1 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 0.0011 ( 1 hom., cov: 32)
Consequence
CUZD1
NM_022034.6 intron
NM_022034.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.117
Genes affected
CUZD1 (HGNC:17937): (CUB and zona pellucida like domains 1) Predicted to be involved in trypsinogen activation. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CUZD1 | NM_022034.6 | c.233+192C>T | intron_variant | ENST00000392790.6 | |||
FAM24B-CUZD1 | NR_037915.1 | n.909+192C>T | intron_variant, non_coding_transcript_variant | ||||
CUZD1 | NR_037912.2 | n.97-1755C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CUZD1 | ENST00000392790.6 | c.233+192C>T | intron_variant | 1 | NM_022034.6 | P1 | |||
CUZD1 | ENST00000338948.3 | c.82+4776C>T | intron_variant, NMD_transcript_variant | 1 | |||||
CUZD1 | ENST00000368900.5 | c.83-1755C>T | intron_variant, NMD_transcript_variant | 1 | |||||
CUZD1 | ENST00000368901.5 | c.83-1755C>T | intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00107 AC: 163AN: 152120Hom.: 1 Cov.: 32
GnomAD3 genomes
?
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163
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152120
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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: 0.00107 AC: 163AN: 152238Hom.: 1 Cov.: 32 AF XY: 0.000954 AC XY: 71AN XY: 74432
GnomAD4 genome
?
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163
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32
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74432
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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