chr19-48965331-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4BS1_Supporting
The NM_000146.4(FTL):c.-177C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000115 in 650,672 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 Uncertain significance (★).
Frequency
Consequence
NM_000146.4 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FTL | NM_000146.4 | c.-177C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 4 | ENST00000331825.11 | NP_000137.2 | ||
FTL | NM_000146.4 | c.-177C>T | 5_prime_UTR_variant | Exon 1 of 4 | ENST00000331825.11 | NP_000137.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FTL | ENST00000331825 | c.-177C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 4 | 1 | NM_000146.4 | ENSP00000366525.2 | |||
FTL | ENST00000331825 | c.-177C>T | 5_prime_UTR_variant | Exon 1 of 4 | 1 | NM_000146.4 | ENSP00000366525.2 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152216Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.000116 AC: 58AN: 498456Hom.: 0 Cov.: 4 AF XY: 0.000127 AC XY: 34AN XY: 267912
GnomAD4 genome AF: 0.000112 AC: 17AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74366
ClinVar
Submissions by phenotype
Hereditary hyperferritinemia with congenital cataracts;C1853578:Neuroferritinopathy Uncertain:1
This variant occurs in a non-coding region of the FTL gene. It does not change the encoded amino acid sequence of the FTL protein. This variant is present in population databases (no rsID available, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with FTL-related conditions. ClinVar contains an entry for this variant (Variation ID: 1415647). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at