NM_005245.4:c.13645G>A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005245.4(FAT1):c.13645G>A(p.Val4549Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000155 in 1,613,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_005245.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAT1 | NM_005245.4 | c.13645G>A | p.Val4549Met | missense_variant | Exon 27 of 27 | ENST00000441802.7 | NP_005236.2 | |
FAT1 | XM_005262834.4 | c.13681G>A | p.Val4561Met | missense_variant | Exon 28 of 28 | XP_005262891.1 | ||
FAT1 | XM_005262835.3 | c.13681G>A | p.Val4561Met | missense_variant | Exon 28 of 28 | XP_005262892.1 | ||
FAT1 | XM_006714139.4 | c.13645G>A | p.Val4549Met | missense_variant | Exon 27 of 27 | XP_006714202.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAT1 | ENST00000441802.7 | c.13645G>A | p.Val4549Met | missense_variant | Exon 27 of 27 | 5 | NM_005245.4 | ENSP00000406229.2 | ||
FAT1 | ENST00000512772.5 | c.982G>A | p.Val328Met | missense_variant | Exon 4 of 4 | 2 | ENSP00000424157.1 | |||
FAT1 | ENST00000500085.2 | n.1337G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249194Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135172
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461708Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727136
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.13645G>A (p.V4549M) alteration is located in exon 27 (coding exon 26) of the FAT1 gene. This alteration results from a G to A substitution at nucleotide position 13645, causing the valine (V) at amino acid position 4549 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at