1-113706071-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001323043.2(PHTF1):c.1490T>C(p.Phe497Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,614,142 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001323043.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHTF1 | NM_001323043.2 | c.1490T>C | p.Phe497Ser | missense_variant | 13/19 | ENST00000369604.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHTF1 | ENST00000369604.6 | c.1490T>C | p.Phe497Ser | missense_variant | 13/19 | 5 | NM_001323043.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251276Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135802
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461776Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727182
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152366Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74508
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2021 | The c.1490T>C (p.F497S) alteration is located in exon 12 (coding exon 12) of the PHTF1 gene. This alteration results from a T to C substitution at nucleotide position 1490, causing the phenylalanine (F) at amino acid position 497 to be replaced by a serine (S). 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