chr12-57716421-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_006812.4(OS9):c.902C>T(p.Pro301Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000334 in 1,556,548 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_006812.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OS9 | NM_006812.4 | c.902C>T | p.Pro301Leu | missense_variant | 8/15 | ENST00000315970.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OS9 | ENST00000315970.12 | c.902C>T | p.Pro301Leu | missense_variant | 8/15 | 1 | NM_006812.4 | P4 | |
ENST00000549477.1 | n.534+4556G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152030Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000910 AC: 15AN: 164914Hom.: 0 AF XY: 0.000104 AC XY: 9AN XY: 86782
GnomAD4 exome AF: 0.0000320 AC: 45AN: 1404400Hom.: 0 Cov.: 31 AF XY: 0.0000375 AC XY: 26AN XY: 693100
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152148Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4AN XY: 74372
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at