chr1-202438085-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000480184.5(PPP1R12B):c.1519A>G(p.Ile507Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00068 in 1,603,458 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000480184.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP1R12B | NM_002481.4 | c.1458+61A>G | intron_variant | ENST00000608999.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP1R12B | ENST00000608999.6 | c.1458+61A>G | intron_variant | 1 | NM_002481.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00296 AC: 450AN: 152066Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000997 AC: 235AN: 235634Hom.: 0 AF XY: 0.000688 AC XY: 88AN XY: 127984
GnomAD4 exome AF: 0.000440 AC: 639AN: 1451274Hom.: 2 Cov.: 31 AF XY: 0.000416 AC XY: 300AN XY: 721424
GnomAD4 genome ? AF: 0.00296 AC: 451AN: 152184Hom.: 3 Cov.: 32 AF XY: 0.00267 AC XY: 199AN XY: 74410
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | PPP1R12B: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at