12-7062270-C-CAAAAA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001734.5(C1S):c.6-193_6-189dupAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.16 ( 1980 hom., cov: 17)
Exomes 𝑓: 0.052 ( 8 hom. )
Failed GnomAD Quality Control
Consequence
C1S
NM_001734.5 intron
NM_001734.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.29
Genes affected
C1S (HGNC:1247): (complement C1s) This gene encodes a serine protease, which is a major constituent of the human complement subcomponent C1. C1s associates with two other complement components C1r and C1q in order to yield the first component of the serum complement system. Defects in this gene are the cause of selective C1s deficiency. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 12-7062270-C-CAAAAA is Benign according to our data. Variant chr12-7062270-C-CAAAAA is described in ClinVar as [Benign]. Clinvar id is 1247086.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C1S | NM_001734.5 | c.6-193_6-189dupAAAAA | intron_variant | Intron 2 of 11 | ENST00000360817.10 | NP_001725.1 | ||
C1S | NM_201442.4 | c.6-193_6-189dupAAAAA | intron_variant | Intron 2 of 11 | NP_958850.1 | |||
C1S | NM_001346850.2 | c.-289+365_-289+369dupAAAAA | intron_variant | Intron 2 of 10 | NP_001333779.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.161 AC: 17210AN: 107172Hom.: 1978 Cov.: 17
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GnomAD4 exome AF: 0.0518 AC: 17007AN: 328544Hom.: 8 Cov.: 0 AF XY: 0.0516 AC XY: 9157AN XY: 177624
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.161 AC: 17213AN: 107176Hom.: 1980 Cov.: 17 AF XY: 0.158 AC XY: 7965AN XY: 50394
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 19, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at