rs1554861288
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_ModeratePM2PP3_ModeratePP5
The NM_025145.7(CFAP43):c.3661-2del variant causes a splice acceptor change. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
CFAP43
NM_025145.7 splice_acceptor
NM_025145.7 splice_acceptor
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.08
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
PVS1
?
Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.021408563 fraction of the gene. Cryptic splice site detected, with MaxEntScore 3.1, offset of -42, new splice context is: tatagaaaatattgtctcAGgtg. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
PP5
?
Variant 10-104147999-CT-C is Pathogenic according to our data. Variant chr10-104147999-CT-C is described in ClinVar as [Pathogenic]. Clinvar id is 523144.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP43 | NM_025145.7 | c.3661-2del | splice_acceptor_variant | ENST00000357060.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP43 | ENST00000357060.8 | c.3661-2del | splice_acceptor_variant | 1 | NM_025145.7 | P1 | |||
CFAP43 | ENST00000434629.5 | c.1743-2del | splice_acceptor_variant | 1 | |||||
CFAP43 | ENST00000457071.5 | c.207-2del | splice_acceptor_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 25
GnomAD4 exome
Cov.:
25
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Spermatogenic failure 19 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 26, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: -1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at