9-128818808-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000372642.5(ENDOG):āc.124G>Cā(p.Val42Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000415 in 1,278,350 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000372642.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ENDOG | NM_004435.2 | c.124G>C | p.Val42Leu | missense_variant | 1/3 | ENST00000372642.5 | NP_004426.2 | |
ENDOG | XM_011518347.3 | c.124G>C | p.Val42Leu | missense_variant | 1/4 | XP_011516649.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENDOG | ENST00000372642.5 | c.124G>C | p.Val42Leu | missense_variant | 1/3 | 1 | NM_004435.2 | ENSP00000361725.4 |
Frequencies
GnomAD3 genomes AF: 0.0000398 AC: 6AN: 150678Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000417 AC: 47AN: 1127672Hom.: 0 Cov.: 33 AF XY: 0.0000426 AC XY: 23AN XY: 540508
GnomAD4 genome AF: 0.0000398 AC: 6AN: 150678Hom.: 0 Cov.: 32 AF XY: 0.0000544 AC XY: 4AN XY: 73498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 01, 2021 | The c.124G>C (p.V42L) alteration is located in exon 1 (coding exon 1) of the ENDOG gene. This alteration results from a G to C substitution at nucleotide position 124, causing the valine (V) at amino acid position 42 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