20-3147039-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021826.5(FASTKD5):c.2032G>A(p.Ala678Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000821 in 1,461,884 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_021826.5 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 |
---|---|---|---|---|---|---|---|---|---|---|
FASTKD5 | ENST00000380266.4 | c.2032G>A | p.Ala678Thr | missense_variant | Exon 2 of 2 | 1 | NM_021826.5 | ENSP00000369618.3 | ||
UBOX5 | ENST00000217173.7 | c.-42+12727G>A | intron_variant | Intron 1 of 4 | 1 | NM_014948.4 | ENSP00000217173.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251316Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135836
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 727242
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2032G>A (p.A678T) alteration is located in exon 2 (coding exon 1) of the FASTKD5 gene. This alteration results from a G to A substitution at nucleotide position 2032, causing the alanine (A) at amino acid position 678 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