chrX-129746638-T-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_003399.6(XPNPEP2):āc.447T>Cā(p.Pro149Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 1,205,591 control chromosomes in the GnomAD database, including 52,644 homozygotes. There are 128,535 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_003399.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XPNPEP2 | ENST00000371106.4 | c.447T>C | p.Pro149Pro | synonymous_variant | Exon 6 of 21 | 1 | NM_003399.6 | ENSP00000360147.3 | ||
XPNPEP2 | ENST00000371105.7 | n.687T>C | non_coding_transcript_exon_variant | Exon 6 of 6 | 2 | |||||
XPNPEP2 | ENST00000681234.1 | n.712T>C | non_coding_transcript_exon_variant | Exon 6 of 7 |
Frequencies
GnomAD3 genomes AF: 0.445 AC: 47915AN: 107644Hom.: 10114 Cov.: 20 AF XY: 0.418 AC XY: 12600AN XY: 30152
GnomAD3 exomes AF: 0.384 AC: 70472AN: 183329Hom.: 10958 AF XY: 0.370 AC XY: 25056AN XY: 67767
GnomAD4 exome AF: 0.318 AC: 348687AN: 1097890Hom.: 42525 Cov.: 32 AF XY: 0.319 AC XY: 115882AN XY: 363380
GnomAD4 genome AF: 0.445 AC: 47973AN: 107701Hom.: 10119 Cov.: 20 AF XY: 0.419 AC XY: 12653AN XY: 30219
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at