20-32210091-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_015352.2(POFUT1):c.145G>A(p.Asp49Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,614,006 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 (★). Synonymous variant affecting the same amino acid position (i.e. D49D) has been classified as Benign.
Frequency
Consequence
NM_015352.2 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 |
---|---|---|---|---|---|---|---|
POFUT1 | NM_015352.2 | c.145G>A | p.Asp49Asn | missense_variant | 2/7 | ENST00000375749.8 | |
POFUT1 | NM_172236.2 | c.145G>A | p.Asp49Asn | missense_variant | 2/5 | ||
POFUT1 | XM_047440079.1 | c.-79+2026G>A | intron_variant | ||||
POFUT1 | XR_007067447.1 | n.207G>A | non_coding_transcript_exon_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POFUT1 | ENST00000375749.8 | c.145G>A | p.Asp49Asn | missense_variant | 2/7 | 1 | NM_015352.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152138Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251480Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135912
GnomAD4 exome AF: 0.0000246 AC: 36AN: 1461868Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727236
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74304
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 02, 2023 | The c.145G>A (p.D49N) alteration is located in exon 2 (coding exon 2) of the POFUT1 gene. This alteration results from a G to A substitution at nucleotide position 145, causing the aspartic acid (D) at amino acid position 49 to be replaced by an asparagine (N). 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