19-5866627-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002034.2(FUT5):c.1099C>T(p.Arg367Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000416 in 1,613,242 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002034.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FUT5 | NM_002034.2 | c.1099C>T | p.Arg367Cys | missense_variant | 2/2 | ENST00000588525.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUT5 | ENST00000588525.1 | c.1099C>T | p.Arg367Cys | missense_variant | 2/2 | 1 | NM_002034.2 | P1 | |
FUT5 | ENST00000252675.6 | c.1099C>T | p.Arg367Cys | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000309 AC: 47AN: 152108Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000355 AC: 89AN: 250382Hom.: 0 AF XY: 0.000420 AC XY: 57AN XY: 135612
GnomAD4 exome AF: 0.000427 AC: 624AN: 1461016Hom.: 0 Cov.: 80 AF XY: 0.000443 AC XY: 322AN XY: 726812
GnomAD4 genome AF: 0.000309 AC: 47AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.1099C>T (p.R367C) alteration is located in exon 2 (coding exon 1) of the FUT5 gene. This alteration results from a C to T substitution at nucleotide position 1099, causing the arginine (R) at amino acid position 367 to be replaced by a cysteine (C). 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