rs11248321
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022034.6(CUZD1):c.1382+69T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 1,330,384 control chromosomes in the GnomAD database, including 188,584 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 0.47 ( 17816 hom., cov: 32)
Exomes 𝑓: 0.53 ( 170768 hom. )
Consequence
CUZD1
NM_022034.6 intron
NM_022034.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.16
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CUZD1 | NM_022034.6 | c.1382+69T>C | intron_variant | ENST00000392790.6 | |||
FAM24B-CUZD1 | NR_037915.1 | n.2058+69T>C | intron_variant, non_coding_transcript_variant | ||||
CUZD1 | NR_037912.2 | n.1245+69T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CUZD1 | ENST00000392790.6 | c.1382+69T>C | intron_variant | 1 | NM_022034.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.466 AC: 70817AN: 151812Hom.: 17819 Cov.: 32
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GnomAD4 exome AF: 0.535 AC: 629949AN: 1178456Hom.: 170768 AF XY: 0.534 AC XY: 308723AN XY: 578508
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GnomAD4 genome ? AF: 0.466 AC: 70828AN: 151928Hom.: 17816 Cov.: 32 AF XY: 0.469 AC XY: 34852AN XY: 74250
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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