8-98123347-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001145860.2(POP1):āc.10G>Cā(p.Ala4Pro) variant causes a missense change. The variant allele was found at a frequency of 0.0000186 in 1,613,412 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 (ā ).
Frequency
Consequence
NM_001145860.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POP1 | NM_001145860.2 | c.10G>C | p.Ala4Pro | missense_variant | Exon 2 of 16 | ENST00000401707.7 | NP_001139332.1 | |
POP1 | NM_001145861.2 | c.10G>C | p.Ala4Pro | missense_variant | Exon 2 of 16 | NP_001139333.1 | ||
POP1 | NM_015029.3 | c.10G>C | p.Ala4Pro | missense_variant | Exon 2 of 16 | NP_055844.2 | ||
POP1 | XM_011516801.3 | c.10G>C | p.Ala4Pro | missense_variant | Exon 2 of 12 | XP_011515103.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POP1 | ENST00000401707.7 | c.10G>C | p.Ala4Pro | missense_variant | Exon 2 of 16 | 2 | NM_001145860.2 | ENSP00000385787.2 | ||
POP1 | ENST00000349693.3 | c.10G>C | p.Ala4Pro | missense_variant | Exon 2 of 16 | 1 | ENSP00000339529.3 | |||
POP1 | ENST00000522319.5 | c.10G>C | p.Ala4Pro | missense_variant | Exon 2 of 5 | 4 | ENSP00000428945.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152096Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251424Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135894
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461316Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727008
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152096Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74298
ClinVar
Submissions by phenotype
not provided Uncertain:1
Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This sequence change replaces alanine with proline at codon 4 of the POP1 protein (p.Ala4Pro). The alanine residue is moderately conserved and there is a small physicochemical difference between alanine and proline. This variant is present in population databases (rs145484648, ExAC 0.002%). This variant has not been reported in the literature in individuals with POP1-related conditions. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at