3-113291671-C-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_001164496.2(CFAP44):c.5451G>A(p.Ala1817=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00015 in 1,537,272 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.00050 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
CFAP44
NM_001164496.2 synonymous
NM_001164496.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.66
Genes affected
CFAP44 (HGNC:25631): (cilia and flagella associated protein 44) Enables peptidase activity. Involved in sperm axoneme assembly. Acts upstream of or within microtubule cytoskeleton organization. Predicted to be located in cytoplasm; cytoskeleton; and motile cilium. Implicated in spermatogenic failure 20. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
Variant 3-113291671-C-T is Benign according to our data. Variant chr3-113291671-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3033995.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-1.66 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFAP44 | NM_001164496.2 | c.5451G>A | p.Ala1817= | synonymous_variant | 35/35 | ENST00000393845.9 | |
LOC127898559 | NR_183046.1 | n.8087G>A | non_coding_transcript_exon_variant | 48/48 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFAP44 | ENST00000393845.9 | c.5451G>A | p.Ala1817= | synonymous_variant | 35/35 | 5 | NM_001164496.2 | P2 | |
CFAP44 | ENST00000484923.1 | n.583G>A | non_coding_transcript_exon_variant | 2/2 | 4 | ||||
CFAP44 | ENST00000461734.1 | c.*141G>A | 3_prime_UTR_variant, NMD_transcript_variant | 10/10 | 2 | ||||
CFAP44 | ENST00000489244.1 | c.*374G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000500 AC: 76AN: 152148Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000123 AC: 18AN: 145780Hom.: 0 AF XY: 0.000142 AC XY: 11AN XY: 77504
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GnomAD4 exome AF: 0.000112 AC: 155AN: 1385006Hom.: 0 Cov.: 34 AF XY: 0.000114 AC XY: 78AN XY: 683420
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GnomAD4 genome AF: 0.000499 AC: 76AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.000403 AC XY: 30AN XY: 74454
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
CFAP44-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 22, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Prediction
BayesDel_noAF
Benign
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Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at