chr8-98127673-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001145860.2(POP1):c.221A>G(p.Gln74Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00074 in 1,614,168 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. Q74Q) has been classified as Likely benign.
Frequency
Consequence
NM_001145860.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POP1 | NM_001145860.2 | c.221A>G | p.Gln74Arg | missense_variant | 3/16 | ENST00000401707.7 | |
POP1 | NM_001145861.2 | c.221A>G | p.Gln74Arg | missense_variant | 3/16 | ||
POP1 | NM_015029.3 | c.221A>G | p.Gln74Arg | missense_variant | 3/16 | ||
POP1 | XM_011516801.3 | c.221A>G | p.Gln74Arg | missense_variant | 3/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POP1 | ENST00000401707.7 | c.221A>G | p.Gln74Arg | missense_variant | 3/16 | 2 | NM_001145860.2 | P1 | |
POP1 | ENST00000349693.3 | c.221A>G | p.Gln74Arg | missense_variant | 3/16 | 1 | P1 | ||
POP1 | ENST00000522319.5 | c.221A>G | p.Gln74Arg | missense_variant | 3/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00391 AC: 595AN: 152188Hom.: 5 Cov.: 31
GnomAD3 exomes AF: 0.00113 AC: 285AN: 251476Hom.: 3 AF XY: 0.000839 AC XY: 114AN XY: 135908
GnomAD4 exome AF: 0.000405 AC: 592AN: 1461862Hom.: 1 Cov.: 31 AF XY: 0.000333 AC XY: 242AN XY: 727232
GnomAD4 genome ? AF: 0.00395 AC: 602AN: 152306Hom.: 5 Cov.: 31 AF XY: 0.00369 AC XY: 275AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at