chr19-5844437-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001382749.2(FUT3):āc.403T>Cā(p.Phe135Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,938 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001382749.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FUT3 | NM_001097639.3 | c.403T>C | p.Phe135Leu | missense_variant | 3/3 | ENST00000709635.1 | |
FUT3 | NM_001382749.2 | c.403T>C | p.Phe135Leu | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUT3 | ENST00000303225.12 | c.403T>C | p.Phe135Leu | missense_variant | 3/3 | 1 | P1 | ||
FUT3 | ENST00000458379.7 | c.403T>C | p.Phe135Leu | missense_variant | 2/2 | 1 | P1 | ||
FUT3 | ENST00000589620.6 | c.403T>C | p.Phe135Leu | missense_variant | 3/3 | 1 | P1 | ||
FUT3 | ENST00000589918.5 | c.403T>C | p.Phe135Leu | missense_variant | 3/3 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000527 AC: 8AN: 151928Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251476Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135916
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461890Hom.: 0 Cov.: 36 AF XY: 0.00000275 AC XY: 2AN XY: 727246
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152048Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 27, 2023 | The c.403T>C (p.F135L) alteration is located in exon 3 (coding exon 1) of the FUT3 gene. This alteration results from a T to C substitution at nucleotide position 403, causing the phenylalanine (F) at amino acid position 135 to be replaced by a leucine (L). 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