chr8-98123347-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001145860.2(POP1):c.10G>A(p.Ala4Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00341 in 1,613,516 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A4P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001145860.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.10G>A | p.Ala4Thr | missense_variant | 2/16 | ENST00000401707.7 | |
POP1 | NM_001145861.2 | c.10G>A | p.Ala4Thr | missense_variant | 2/16 | ||
POP1 | NM_015029.3 | c.10G>A | p.Ala4Thr | missense_variant | 2/16 | ||
POP1 | XM_011516801.3 | c.10G>A | p.Ala4Thr | missense_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POP1 | ENST00000401707.7 | c.10G>A | p.Ala4Thr | missense_variant | 2/16 | 2 | NM_001145860.2 | P1 | |
POP1 | ENST00000349693.3 | c.10G>A | p.Ala4Thr | missense_variant | 2/16 | 1 | P1 | ||
POP1 | ENST00000522319.5 | c.10G>A | p.Ala4Thr | missense_variant | 2/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00193 AC: 294AN: 152096Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00556 AC: 1397AN: 251424Hom.: 26 AF XY: 0.00711 AC XY: 966AN XY: 135894
GnomAD4 exome AF: 0.00356 AC: 5208AN: 1461302Hom.: 77 Cov.: 31 AF XY: 0.00450 AC XY: 3272AN XY: 727006
GnomAD4 genome ? AF: 0.00192 AC: 292AN: 152214Hom.: 3 Cov.: 32 AF XY: 0.00228 AC XY: 170AN XY: 74426
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at