7-77910381-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001366089.1(PHTF2):c.748C>T(p.Leu250Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000479 in 1,460,810 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_001366089.1 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHTF2 | NM_001366089.1 | c.748C>T | p.Leu250Phe | missense_variant | Exon 8 of 19 | NP_001353018.1 | ||
PHTF2 | NM_001127357.2 | c.646C>T | p.Leu216Phe | missense_variant | Exon 7 of 18 | NP_001120829.1 | ||
PHTF2 | NM_001395272.1 | c.646C>T | p.Leu216Phe | missense_variant | Exon 8 of 19 | NP_001382201.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248340Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134690
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460810Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726616
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.646C>T (p.L216F) alteration is located in exon 7 (coding exon 7) of the PHTF2 gene. This alteration results from a C to T substitution at nucleotide position 646, causing the leucine (L) at amino acid position 216 to be replaced by a phenylalanine (F). 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