rs2230267
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_000146.4(FTL):c.163T>C(p.Leu55Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 1,613,848 control chromosomes in the GnomAD database, including 222,359 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000146.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FTL | NM_000146.4 | c.163T>C | p.Leu55Leu | synonymous_variant | Exon 2 of 4 | ENST00000331825.11 | NP_000137.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.509 AC: 77408AN: 151996Hom.: 19855 Cov.: 33
GnomAD3 exomes AF: 0.501 AC: 125886AN: 251284Hom.: 32088 AF XY: 0.499 AC XY: 67846AN XY: 135854
GnomAD4 exome AF: 0.524 AC: 765999AN: 1461732Hom.: 202487 Cov.: 53 AF XY: 0.521 AC XY: 379096AN XY: 727186
GnomAD4 genome AF: 0.509 AC: 77466AN: 152116Hom.: 19872 Cov.: 33 AF XY: 0.503 AC XY: 37402AN XY: 74348
ClinVar
Submissions by phenotype
not specified Benign:8
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This variant is classified as Benign based on local population frequency. This variant was detected in 74% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy, Progressive Myoclonus Epilepsy and Abnormal Movements and Neurodegeneration with brain iron accumulation. Number of patients: 69. Only high quality variants are reported. -
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Hereditary hyperferritinemia with congenital cataracts Benign:3
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Neuroferritinopathy Benign:2
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not provided Benign:2
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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. -
sporadic abdominal aortic aneurysm Pathogenic:1
Observed frequency is 15/19 = 0.789 patients with abdominal aortic aneurysm versus heterozygosity is described in "Variation Viewer" as 0.496. -
Hereditary hyperferritinemia with congenital cataracts;C1853578:Neuroferritinopathy Benign:1
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Glycogen storage disease due to muscle and heart glycogen synthase deficiency Benign:1
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L-ferritin deficiency Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at