chr7-100307926-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001004351.5(SPDYE3):c.41C>T(p.Pro14Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000209 in 1,432,612 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001004351.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPDYE3 | NM_001004351.5 | c.41C>T | p.Pro14Leu | missense_variant | 1/11 | ENST00000332397.6 | |
SPDYE3 | XM_047420404.1 | c.41C>T | p.Pro14Leu | missense_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPDYE3 | ENST00000332397.6 | c.41C>T | p.Pro14Leu | missense_variant | 1/11 | 1 | NM_001004351.5 | P1 | |
ENST00000685724.2 | n.751-7203G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD4 exome AF: 0.00000209 AC: 3AN: 1432612Hom.: 0 Cov.: 31 AF XY: 0.00000281 AC XY: 2AN XY: 711726
GnomAD4 genome Cov.: 30
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at