1-160276914-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002857.4(PEX19):c.*2637G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0265 in 449,832 control chromosomes in the GnomAD database, including 263 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002857.4 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PEX19 | NM_002857.4 | c.*2637G>A | 3_prime_UTR_variant | Exon 8 of 8 | ENST00000368072.10 | NP_002848.1 | ||
PEX19 | NM_001193644.1 | c.*2645G>A | 3_prime_UTR_variant | Exon 8 of 8 | NP_001180573.1 | |||
PEX19 | NR_036492.2 | n.3436G>A | non_coding_transcript_exon_variant | Exon 7 of 7 | ||||
PEX19 | NR_036493.2 | n.3460G>A | non_coding_transcript_exon_variant | Exon 7 of 7 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0242 AC: 3675AN: 152120Hom.: 62 Cov.: 32
GnomAD3 exomes AF: 0.0308 AC: 3981AN: 129128Hom.: 90 AF XY: 0.0325 AC XY: 2291AN XY: 70426
GnomAD4 exome AF: 0.0277 AC: 8255AN: 297594Hom.: 200 Cov.: 0 AF XY: 0.0300 AC XY: 5077AN XY: 169200
GnomAD4 genome AF: 0.0242 AC: 3678AN: 152238Hom.: 63 Cov.: 32 AF XY: 0.0252 AC XY: 1879AN XY: 74432
ClinVar
Submissions by phenotype
not provided Benign:1
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Peroxisome biogenesis disorder 12A (Zellweger) Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at