chr8-98123345-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001145860.2(POP1):c.8A>G(p.Asn3Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,613,694 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145860.2 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 |
---|---|---|---|---|---|---|---|
POP1 | NM_001145860.2 | c.8A>G | p.Asn3Ser | missense_variant | 2/16 | ENST00000401707.7 | |
POP1 | NM_001145861.2 | c.8A>G | p.Asn3Ser | missense_variant | 2/16 | ||
POP1 | NM_015029.3 | c.8A>G | p.Asn3Ser | missense_variant | 2/16 | ||
POP1 | XM_011516801.3 | c.8A>G | p.Asn3Ser | missense_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POP1 | ENST00000401707.7 | c.8A>G | p.Asn3Ser | missense_variant | 2/16 | 2 | NM_001145860.2 | P1 | |
POP1 | ENST00000349693.3 | c.8A>G | p.Asn3Ser | missense_variant | 2/16 | 1 | P1 | ||
POP1 | ENST00000522319.5 | c.8A>G | p.Asn3Ser | missense_variant | 2/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251434Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135902
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461402Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727024
GnomAD4 genome ? AF: 0.000177 AC: 27AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74466
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 17, 2023 | An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 3 of the POP1 protein (p.Asn3Ser). This variant is present in population databases (rs188031074, gnomAD 0.06%). This variant has not been reported in the literature in individuals affected with POP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 2171220). 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at