4-186588729-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_005245.4(FAT1):c.13630G>A(p.Ala4544Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,844 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAT1 | NM_005245.4 | c.13630G>A | p.Ala4544Thr | missense_variant | Exon 27 of 27 | ENST00000441802.7 | NP_005236.2 | |
FAT1 | XM_005262834.4 | c.13666G>A | p.Ala4556Thr | missense_variant | Exon 28 of 28 | XP_005262891.1 | ||
FAT1 | XM_005262835.3 | c.13666G>A | p.Ala4556Thr | missense_variant | Exon 28 of 28 | XP_005262892.1 | ||
FAT1 | XM_006714139.4 | c.13630G>A | p.Ala4544Thr | 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.13630G>A | p.Ala4544Thr | missense_variant | Exon 27 of 27 | 5 | NM_005245.4 | ENSP00000406229.2 | ||
FAT1 | ENST00000512772.5 | c.967G>A | p.Ala323Thr | missense_variant | Exon 4 of 4 | 2 | ENSP00000424157.1 | |||
FAT1 | ENST00000500085.2 | n.1322G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 249212Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135176
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461710Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727136
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74328
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.13630G>A (p.A4544T) 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 13630, causing the alanine (A) at amino acid position 4544 to be replaced by a threonine (T). 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