chr3-119706843-T-C
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_033364.4(CFAP91):āc.159T>Cā(p.His53His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,613,382 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 (ā ).
Frequency
Genomes: š 0.00011 ( 0 hom., cov: 30)
Exomes š: 0.00011 ( 0 hom. )
Consequence
CFAP91
NM_033364.4 synonymous
NM_033364.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0280
Genes affected
CFAP91 (HGNC:24010): (cilia and flagella associated protein 91) Predicted to be involved in cilium movement. Predicted to be located in axoneme and motile cilium. Predicted to colocalize with radial spoke stalk. Implicated in spermatogenic failure 51. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 3-119706843-T-C is Benign according to our data. Variant chr3-119706843-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3025363.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.028 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CFAP91 | NM_033364.4 | c.159T>C | p.His53His | synonymous_variant | 2/18 | ENST00000273390.9 | NP_203528.3 | |
CFAP91 | NM_001320316.2 | c.99T>C | p.His33His | synonymous_variant | 2/18 | NP_001307245.2 | ||
CFAP91 | NM_001320317.2 | c.16-561T>C | intron_variant | NP_001307246.2 | ||||
CFAP91 | NM_001320318.2 | c.-19-1748T>C | intron_variant | NP_001307247.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CFAP91 | ENST00000273390.9 | c.159T>C | p.His53His | synonymous_variant | 2/18 | 1 | NM_033364.4 | ENSP00000273390.5 | ||
ENSG00000285585 | ENST00000648112.1 | c.159T>C | p.His53His | synonymous_variant | 2/18 | ENSP00000497876.1 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 151670Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.000155 AC: 39AN: 251446Hom.: 0 AF XY: 0.000147 AC XY: 20AN XY: 135900
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GnomAD4 exome AF: 0.000112 AC: 164AN: 1461712Hom.: 0 Cov.: 29 AF XY: 0.000124 AC XY: 90AN XY: 727162
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GnomAD4 genome AF: 0.000105 AC: 16AN: 151670Hom.: 0 Cov.: 30 AF XY: 0.0000945 AC XY: 7AN XY: 74036
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | CFAP91: BP4, BP7 - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at