chr1-156903934-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001080471.3(PEAR1):c.8C>T(p.Pro3Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000799 in 1,613,934 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 Likely benign (★).
Frequency
Consequence
NM_001080471.3 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEAR1 | NM_001080471.3 | c.8C>T | p.Pro3Leu | missense_variant | 2/23 | ENST00000292357.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEAR1 | ENST00000292357.8 | c.8C>T | p.Pro3Leu | missense_variant | 2/23 | 5 | NM_001080471.3 | P1 | |
PEAR1 | ENST00000338302.7 | c.8C>T | p.Pro3Leu | missense_variant | 3/24 | 5 | P1 | ||
PEAR1 | ENST00000455314.5 | c.8C>T | p.Pro3Leu | missense_variant | 2/6 | 2 | |||
PEAR1 | ENST00000444016.5 | c.8C>T | p.Pro3Leu | missense_variant, NMD_transcript_variant | 2/7 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251302Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135838
GnomAD4 exome AF: 0.0000828 AC: 121AN: 1461654Hom.: 0 Cov.: 30 AF XY: 0.0000756 AC XY: 55AN XY: 727160
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152280Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74448
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at