14-24131619-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_203402.3(FITM1):c.56C>T(p.Ala19Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000597 in 1,610,636 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_203402.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FITM1 | ENST00000267426.6 | c.56C>T | p.Ala19Val | missense_variant | Exon 1 of 2 | 1 | NM_203402.3 | ENSP00000267426.5 | ||
ENSG00000259371 | ENST00000558325.2 | c.638C>T | p.Ala213Val | missense_variant | Exon 4 of 4 | 5 | ENSP00000453089.2 |
Frequencies
GnomAD3 genomes AF: 0.000480 AC: 73AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000529 AC: 129AN: 244002Hom.: 0 AF XY: 0.000482 AC XY: 64AN XY: 132744
GnomAD4 exome AF: 0.000610 AC: 889AN: 1458312Hom.: 1 Cov.: 34 AF XY: 0.000615 AC XY: 446AN XY: 725166
GnomAD4 genome AF: 0.000479 AC: 73AN: 152324Hom.: 0 Cov.: 33 AF XY: 0.000456 AC XY: 34AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.56C>T (p.A19V) alteration is located in exon 1 (coding exon 1) of the FITM1 gene. This alteration results from a C to T substitution at nucleotide position 56, causing the alanine (A) at amino acid position 19 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at