chr1-156908133-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001080471.3(PEAR1):c.908G>T(p.Arg303Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000451 in 1,597,802 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001080471.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEAR1 | NM_001080471.3 | c.908G>T | p.Arg303Leu | missense_variant | 9/23 | ENST00000292357.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEAR1 | ENST00000292357.8 | c.908G>T | p.Arg303Leu | missense_variant | 9/23 | 5 | NM_001080471.3 | P1 | |
PEAR1 | ENST00000338302.7 | c.908G>T | p.Arg303Leu | missense_variant | 10/24 | 5 | P1 | ||
PEAR1 | ENST00000469390.5 | n.636G>T | non_coding_transcript_exon_variant | 4/18 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000992 AC: 23AN: 231876Hom.: 0 AF XY: 0.0000947 AC XY: 12AN XY: 126768
GnomAD4 exome AF: 0.0000367 AC: 53AN: 1445502Hom.: 0 Cov.: 36 AF XY: 0.0000390 AC XY: 28AN XY: 717406
GnomAD4 genome AF: 0.000125 AC: 19AN: 152300Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.908G>T (p.R303L) alteration is located in exon 9 (coding exon 8) of the PEAR1 gene. This alteration results from a G to T substitution at nucleotide position 908, causing the arginine (R) at amino acid position 303 to be replaced by a leucine (L). 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