chr19-48750910-G-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001384359.1(FUT1):āc.372C>Gā(p.Phe124Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000093 in 1,612,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_001384359.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FUT1 | NM_001384359.1 | c.372C>G | p.Phe124Leu | missense_variant | 2/2 | ENST00000645652.2 | |
FUT1 | NM_000148.4 | c.372C>G | p.Phe124Leu | missense_variant | 4/4 | ||
FUT1 | NM_001329877.1 | c.372C>G | p.Phe124Leu | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUT1 | ENST00000645652.2 | c.372C>G | p.Phe124Leu | missense_variant | 2/2 | NM_001384359.1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000360 AC: 9AN: 250226Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135448
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1460750Hom.: 0 Cov.: 33 AF XY: 0.00000963 AC XY: 7AN XY: 726562
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 12, 2023 | The c.372C>G (p.F124L) alteration is located in exon 4 (coding exon 1) of the FUT1 gene. This alteration results from a C to G substitution at nucleotide position 372, causing the phenylalanine (F) at amino acid position 124 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