chr6-138107131-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_022121.5(PERP):āc.210G>Cā(p.Glu70Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000412 in 1,603,788 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_022121.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PERP | NM_022121.5 | c.210G>C | p.Glu70Asp | missense_variant | 1/3 | ENST00000421351.4 | NP_071404.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PERP | ENST00000421351.4 | c.210G>C | p.Glu70Asp | missense_variant | 1/3 | 1 | NM_022121.5 | ENSP00000397157 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000852 AC: 2AN: 234872Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 129196
GnomAD4 exome AF: 0.0000434 AC: 63AN: 1451686Hom.: 0 Cov.: 32 AF XY: 0.0000360 AC XY: 26AN XY: 721764
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74280
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 17, 2023 | The c.210G>C (p.E70D) alteration is located in exon 1 (coding exon 1) of the PERP gene. This alteration results from a G to C substitution at nucleotide position 210, causing the glutamic acid (E) at amino acid position 70 to be replaced by an aspartic acid (D). 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