13-32134913-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_023037.3(FRY):c.895C>T(p.His299Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000162 in 1,604,324 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_023037.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FRY | ENST00000542859.6 | c.895C>T | p.His299Tyr | missense_variant | Exon 9 of 61 | 5 | NM_023037.3 | ENSP00000445043.2 | ||
FRY | ENST00000647500.1 | c.1030C>T | p.His344Tyr | missense_variant | Exon 9 of 61 | ENSP00000494761.1 | ||||
FRY | ENST00000642040.1 | c.895C>T | p.His299Tyr | missense_variant | Exon 9 of 62 | ENSP00000493189.1 | ||||
FRY | ENST00000645780.1 | c.745C>T | p.His249Tyr | missense_variant | Exon 10 of 62 | ENSP00000494080.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249484Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135360
GnomAD4 exome AF: 0.0000145 AC: 21AN: 1452128Hom.: 0 Cov.: 30 AF XY: 0.0000194 AC XY: 14AN XY: 723066
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.895C>T (p.H299Y) alteration is located in exon 9 (coding exon 9) of the FRY gene. This alteration results from a C to T substitution at nucleotide position 895, causing the histidine (H) at amino acid position 299 to be replaced by a tyrosine (Y). 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