chr19-48703369-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_000511.6(FUT2):c.413G>A(p.Arg138His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,460,860 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R138C) has been classified as Uncertain significance.
Frequency
Consequence
NM_000511.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FUT2 | NM_000511.6 | c.413G>A | p.Arg138His | missense_variant | 2/2 | ENST00000425340.3 | |
LOC105447645 | NR_131188.1 | n.480C>T | non_coding_transcript_exon_variant | 1/1 | |||
FUT2 | NM_001097638.3 | c.413G>A | p.Arg138His | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUT2 | ENST00000425340.3 | c.413G>A | p.Arg138His | missense_variant | 2/2 | 1 | NM_000511.6 | P1 | |
FUT2 | ENST00000522966.2 | c.413G>A | p.Arg138His | missense_variant | 2/2 | 2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250482Hom.: 1 AF XY: 0.0000147 AC XY: 2AN XY: 135638
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460860Hom.: 1 Cov.: 76 AF XY: 0.00000275 AC XY: 2AN XY: 726694
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.413G>A (p.R138H) alteration is located in exon 2 (coding exon 1) of the FUT2 gene. This alteration results from a G to A substitution at nucleotide position 413, causing the arginine (R) at amino acid position 138 to be replaced by a histidine (H). 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