7-102554443-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001396242.1(SPDYE2):c.245C>T(p.Pro82Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001396242.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPDYE2 | NM_001396242.1 | c.245C>T | p.Pro82Leu | missense_variant | Exon 3 of 9 | ENST00000691607.2 | NP_001383171.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPDYE2 | ENST00000691607.2 | c.245C>T | p.Pro82Leu | missense_variant | Exon 3 of 9 | NM_001396242.1 | ENSP00000509749.1 | |||
ENSG00000270249 | ENST00000514917.3 | c.748+12139G>A | intron_variant | Intron 6 of 6 | 3 | ENSP00000423309.4 | ||||
POLR2J3 | ENST00000513506.6 | c.382+12139G>A | intron_variant | Intron 4 of 6 | 5 | ENSP00000421085.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151988Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.0000196 AC: 1AN: 51026Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 25686
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000118 AC: 17AN: 1441676Hom.: 0 Cov.: 38 AF XY: 0.0000139 AC XY: 10AN XY: 717276
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000131 AC: 2AN: 152106Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.245C>T (p.P82L) alteration is located in exon 3 (coding exon 2) of the SPDYE2 gene. This alteration results from a C to T substitution at nucleotide position 245, causing the proline (P) at amino acid position 82 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