chr7-100313164-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001004351.5(SPDYE3):c.788C>T(p.Pro263Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/19 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. P263Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001004351.5 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 |
---|---|---|---|---|---|---|---|
SPDYE3 | NM_001004351.5 | c.788C>T | p.Pro263Leu | missense_variant | 5/11 | ENST00000332397.6 | |
SPDYE3 | XM_047420404.1 | c.788C>T | p.Pro263Leu | missense_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPDYE3 | ENST00000332397.6 | c.788C>T | p.Pro263Leu | missense_variant | 5/11 | 1 | NM_001004351.5 | P1 | |
ENST00000685724.2 | n.751-12441G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 129778Hom.: 0 Cov.: 16 FAILED QC
GnomAD3 exomes AF: 0.0000237 AC: 1AN: 42232Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 21384
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000129 AC: 10AN: 773764Hom.: 0 Cov.: 11 AF XY: 0.0000127 AC XY: 5AN XY: 395078
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000770 AC: 1AN: 129888Hom.: 0 Cov.: 16 AF XY: 0.0000162 AC XY: 1AN XY: 61916
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 11, 2023 | The c.788C>T (p.P263L) alteration is located in exon 5 (coding exon 5) of the SPDYE3 gene. This alteration results from a C to T substitution at nucleotide position 788, causing the proline (P) at amino acid position 263 to be replaced by a leucine (L). 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