rs10927786
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_007272.3(CTRC):c.640-35G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000996 in 1,606,902 control chromosomes in the GnomAD database, including 2 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 0.000072 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00010 ( 1 hom. )
Consequence
CTRC
NM_007272.3 intron
NM_007272.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.145
Genes affected
CTRC (HGNC:2523): (chymotrypsin C) This gene encodes a member of the peptidase S1 family. The encoded protein is a serum calcium-decreasing factor that has chymotrypsin-like protease activity. Alternatively spliced transcript variants have been observed, but their full-length nature has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTRC | NM_007272.3 | c.640-35G>A | intron_variant | ENST00000375949.5 | |||
CTRC | XM_011540550.2 | c.494-35G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTRC | ENST00000375949.5 | c.640-35G>A | intron_variant | 1 | NM_007272.3 | P1 | |||
CTRC | ENST00000375943.6 | c.*94-35G>A | intron_variant | 1 | |||||
CTRC | ENST00000483406.1 | n.404-35G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000724 AC: 11AN: 151976Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000100 AC: 25AN: 248758Hom.: 1 AF XY: 0.0000816 AC XY: 11AN XY: 134792
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GnomAD4 exome AF: 0.000102 AC: 149AN: 1454810Hom.: 1 Cov.: 33 AF XY: 0.0000941 AC XY: 68AN XY: 722940
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GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152092Hom.: 1 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74364
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ClinVar
Not reported inComputational scores
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Benign
CADD
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DANN
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at