19-5844027-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_000149.4(FUT3):c.813C>T(p.Pro271Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 151,794 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_000149.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FUT3 | NM_000149.4 | c.813C>T | p.Pro271Pro | synonymous_variant | Exon 3 of 3 | NP_000140.1 | ||
FUT3 | NM_001097639.3 | c.813C>T | p.Pro271Pro | synonymous_variant | Exon 3 of 3 | NP_001091108.3 | ||
FUT3 | NM_001097640.3 | c.813C>T | p.Pro271Pro | synonymous_variant | Exon 3 of 3 | NP_001091109.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FUT3 | ENST00000303225.12 | c.813C>T | p.Pro271Pro | synonymous_variant | Exon 3 of 3 | 1 | ENSP00000305603.5 | |||
FUT3 | ENST00000458379.7 | c.813C>T | p.Pro271Pro | synonymous_variant | Exon 2 of 2 | 1 | ENSP00000416443.1 | |||
FUT3 | ENST00000589620.6 | c.813C>T | p.Pro271Pro | synonymous_variant | Exon 3 of 3 | 1 | ENSP00000465804.1 | |||
FUT3 | ENST00000589918.5 | c.813C>T | p.Pro271Pro | synonymous_variant | Exon 3 of 3 | 1 | ENSP00000468123.1 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151794Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000829 AC: 2AN: 241342Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131826
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000616 AC: 9AN: 1461650Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3AN XY: 727132
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151794Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74100
ClinVar
Submissions by phenotype
FUT3-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at