19-7629831-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001171155.2(PET100):c.-3G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000521 in 1,536,604 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001171155.2 5_prime_UTR
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PET100 | NM_001171155.2 | c.-3G>A | 5_prime_UTR_variant | Exon 1 of 4 | ENST00000594797.6 | NP_001164626.1 | ||
STXBP2 | NM_001414484.1 | c.-200G>A | 5_prime_UTR_variant | Exon 1 of 21 | NP_001401413.1 | |||
PET100 | NR_033242.2 | n.39G>A | non_coding_transcript_exon_variant | Exon 1 of 5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PET100 | ENST00000594797 | c.-3G>A | 5_prime_UTR_variant | Exon 1 of 4 | 1 | NM_001171155.2 | ENSP00000470539.1 | |||
ENSG00000268400 | ENST00000698368.1 | n.-3G>A | non_coding_transcript_exon_variant | Exon 1 of 20 | ENSP00000513686.1 | |||||
ENSG00000268400 | ENST00000698368.1 | n.-3G>A | 5_prime_UTR_variant | Exon 1 of 20 | ENSP00000513686.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152188Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000720 AC: 1AN: 138818Hom.: 0 AF XY: 0.0000134 AC XY: 1AN XY: 74434
GnomAD4 exome AF: 0.00000361 AC: 5AN: 1384416Hom.: 0 Cov.: 31 AF XY: 0.00000439 AC XY: 3AN XY: 683156
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152188Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74338
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at