chr1-156909841-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001080471.3(PEAR1):c.1502T>C(p.Val501Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000205 in 1,613,782 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 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.1502T>C | p.Val501Ala | missense_variant | 12/23 | ENST00000292357.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEAR1 | ENST00000292357.8 | c.1502T>C | p.Val501Ala | missense_variant | 12/23 | 5 | NM_001080471.3 | P1 | |
PEAR1 | ENST00000338302.7 | c.1502T>C | p.Val501Ala | missense_variant | 13/24 | 5 | P1 | ||
PEAR1 | ENST00000469390.5 | n.1230T>C | non_coding_transcript_exon_variant | 7/18 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000223 AC: 34AN: 152186Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000430 AC: 108AN: 251136Hom.: 0 AF XY: 0.000413 AC XY: 56AN XY: 135754
GnomAD4 exome AF: 0.000203 AC: 297AN: 1461596Hom.: 0 Cov.: 33 AF XY: 0.000195 AC XY: 142AN XY: 727078
GnomAD4 genome ? AF: 0.000223 AC: 34AN: 152186Hom.: 1 Cov.: 33 AF XY: 0.000229 AC XY: 17AN XY: 74370
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 14, 2023 | 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