chr4-186588650-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_005245.4(FAT1):c.13709G>A(p.Gly4570Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,718 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAT1 | NM_005245.4 | c.13709G>A | p.Gly4570Asp | missense_variant | Exon 27 of 27 | ENST00000441802.7 | NP_005236.2 | |
FAT1 | XM_005262834.4 | c.13745G>A | p.Gly4582Asp | missense_variant | Exon 28 of 28 | XP_005262891.1 | ||
FAT1 | XM_005262835.3 | c.13745G>A | p.Gly4582Asp | missense_variant | Exon 28 of 28 | XP_005262892.1 | ||
FAT1 | XM_006714139.4 | c.13709G>A | p.Gly4570Asp | 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.13709G>A | p.Gly4570Asp | missense_variant | Exon 27 of 27 | 5 | NM_005245.4 | ENSP00000406229.2 | ||
FAT1 | ENST00000512772.5 | c.1046G>A | p.Gly349Asp | missense_variant | Exon 4 of 4 | 2 | ENSP00000424157.1 | |||
FAT1 | ENST00000500085.2 | n.1401G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 | |||||
FAT1 | ENST00000507105.1 | c.*157G>A | downstream_gene_variant | 3 | ENSP00000423801.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000805 AC: 2AN: 248562Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134824
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461560Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727046
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74320
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.13709G>A (p.G4570D) 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 13709, causing the glycine (G) at amino acid position 4570 to be replaced by an aspartic acid (D). 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