1-156904815-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001080471.3(PEAR1):c.169C>T(p.Arg57Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,492 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R57Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001080471.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PEAR1 | ENST00000292357.8 | c.169C>T | p.Arg57Trp | missense_variant | Exon 3 of 23 | 5 | NM_001080471.3 | ENSP00000292357.7 | ||
PEAR1 | ENST00000338302.7 | c.169C>T | p.Arg57Trp | missense_variant | Exon 4 of 24 | 5 | ENSP00000344465.3 | |||
PEAR1 | ENST00000455314.5 | c.169C>T | p.Arg57Trp | missense_variant | Exon 3 of 6 | 2 | ENSP00000389742.1 | |||
PEAR1 | ENST00000444016.5 | n.169C>T | non_coding_transcript_exon_variant | Exon 3 of 7 | 3 | ENSP00000397870.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250666Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135474
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461492Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727058
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.169C>T (p.R57W) alteration is located in exon 3 (coding exon 2) of the PEAR1 gene. This alteration results from a C to T substitution at nucleotide position 169, causing the arginine (R) at amino acid position 57 to be replaced by a tryptophan (W). 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