rs11646677
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_006324.3(CFDP1):c.650+20007A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 30)
Failed GnomAD Quality Control
Consequence
CFDP1
NM_006324.3 intron
NM_006324.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.658
Genes affected
CFDP1 (HGNC:1873): (craniofacial development protein 1) Predicted to act upstream of or within several processes, including cell adhesion; negative regulation of fibroblast apoptotic process; and regulation of cell shape. Predicted to be located in kinetochore. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.62).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFDP1 | NM_006324.3 | c.650+20007A>T | intron_variant | ENST00000283882.4 | |||
CFDP1 | XM_011522814.3 | c.651-2515A>T | intron_variant | ||||
CFDP1 | XR_007064846.1 | n.930+16297A>T | intron_variant, non_coding_transcript_variant | ||||
CFDP1 | XR_007064847.1 | n.1045+1566A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFDP1 | ENST00000283882.4 | c.650+20007A>T | intron_variant | 1 | NM_006324.3 | P1 | |||
CFDP1 | ENST00000612761.1 | c.31-2515A>T | intron_variant | 3 | |||||
CFDP1 | ENST00000569341.1 | c.*117-2515A>T | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 151226Hom.: 0 Cov.: 30 FAILED QC
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 151226Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 73766
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?
Data not reliable, filtered out with message: AC0;AS_VQSR
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ClinVar
Not reported inComputational scores
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Name
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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