chr1-156904816-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001080471.3(PEAR1):c.170G>A(p.Arg57Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,774 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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.170G>A | p.Arg57Gln | missense_variant | 3/23 | ENST00000292357.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEAR1 | ENST00000292357.8 | c.170G>A | p.Arg57Gln | missense_variant | 3/23 | 5 | NM_001080471.3 | P1 | |
PEAR1 | ENST00000338302.7 | c.170G>A | p.Arg57Gln | missense_variant | 4/24 | 5 | P1 | ||
PEAR1 | ENST00000455314.5 | c.170G>A | p.Arg57Gln | missense_variant | 3/6 | 2 | |||
PEAR1 | ENST00000444016.5 | c.170G>A | p.Arg57Gln | missense_variant, NMD_transcript_variant | 3/7 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152124Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250646Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135446
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461532Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727066
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152242Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74436
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 25, 2023 | The c.170G>A (p.R57Q) alteration is located in exon 3 (coding exon 2) of the PEAR1 gene. This alteration results from a G to A substitution at nucleotide position 170, causing the arginine (R) at amino acid position 57 to be replaced by a glutamine (Q). 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