rs199607550
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032545.4(CFC1):c.61A>C(p.Asn21His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00896 in 1,099,662 control chromosomes in the GnomAD database, including 213 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. N21N) has been classified as Benign.
Frequency
Consequence
NM_032545.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CFC1 | NM_032545.4 | c.61A>C | p.Asn21His | missense_variant | 2/6 | ENST00000259216.6 | |
CFC1 | NM_001270420.2 | c.61A>C | p.Asn21His | missense_variant | 2/5 | ||
CFC1 | NM_001270421.2 | c.61A>C | p.Asn21His | missense_variant | 2/4 | ||
CFC1 | XM_011511486.4 | c.61A>C | p.Asn21His | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFC1 | ENST00000259216.6 | c.61A>C | p.Asn21His | missense_variant | 2/6 | 1 | NM_032545.4 | P1 | |
CFC1 | ENST00000615342.4 | c.61A>C | p.Asn21His | missense_variant | 2/5 | 5 | |||
CFC1 | ENST00000621673.4 | c.61A>C | p.Asn21His | missense_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0393 AC: 5193AN: 132174Hom.: 103 Cov.: 19
GnomAD3 exomes AF: 0.0125 AC: 1535AN: 122496Hom.: 46 AF XY: 0.0106 AC XY: 692AN XY: 64980
GnomAD4 exome AF: 0.00480 AC: 4645AN: 967394Hom.: 109 Cov.: 13 AF XY: 0.00409 AC XY: 1997AN XY: 488434
GnomAD4 genome ? AF: 0.0394 AC: 5208AN: 132268Hom.: 104 Cov.: 19 AF XY: 0.0376 AC XY: 2389AN XY: 63478
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 07, 2013 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jul 22, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at