19-49426692-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001195256.2(GFY):c.262C>T(p.Pro88Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000795 in 1,384,014 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict 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. P88L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001195256.2 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 |
---|---|---|---|---|---|---|---|
GFY | NM_001195256.2 | c.262C>T | p.Pro88Ser | missense_variant | 2/4 | ENST00000610896.3 | |
GFY | NM_001385187.1 | c.262C>T | p.Pro88Ser | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GFY | ENST00000610896.3 | c.262C>T | p.Pro88Ser | missense_variant | 2/4 | 2 | NM_001195256.2 | P1 | |
GFY | ENST00000576655.5 | c.262C>T | p.Pro88Ser | missense_variant | 3/5 | 5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000795 AC: 11AN: 1384014Hom.: 0 Cov.: 31 AF XY: 0.00000732 AC XY: 5AN XY: 682938
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2022 | The c.262C>T (p.P88S) alteration is located in exon 1 (coding exon 1) of the GFY gene. This alteration results from a C to T substitution at nucleotide position 262, causing the proline (P) at amino acid position 88 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