rs761504767
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_022098.4(XPNPEP3):āc.1122C>Gā(p.Leu374=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,644 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L374L) has been classified as Likely benign.
Frequency
Consequence
NM_022098.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XPNPEP3 | NM_022098.4 | c.1122C>G | p.Leu374= | synonymous_variant | 8/10 | ENST00000357137.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XPNPEP3 | ENST00000357137.9 | c.1122C>G | p.Leu374= | synonymous_variant | 8/10 | 1 | NM_022098.4 | P1 | |
XPNPEP3 | ENST00000428799.1 | c.*1004C>G | 3_prime_UTR_variant, NMD_transcript_variant | 9/11 | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251132Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135736
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461644Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727130
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at