chr12-105366648-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001145199.2(C12orf75):c.139T>C(p.Ser47Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000628 in 1,544,358 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145199.2 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 |
---|---|---|---|---|---|---|---|
C12orf75 | NM_001145199.2 | c.139T>C | p.Ser47Pro | missense_variant | 4/6 | ENST00000443585.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C12orf75 | ENST00000443585.6 | c.139T>C | p.Ser47Pro | missense_variant | 4/6 | 2 | NM_001145199.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000296 AC: 45AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000846 AC: 13AN: 153574Hom.: 0 AF XY: 0.0000245 AC XY: 2AN XY: 81528
GnomAD4 exome AF: 0.0000374 AC: 52AN: 1392034Hom.: 0 Cov.: 26 AF XY: 0.0000335 AC XY: 23AN XY: 687132
GnomAD4 genome ? AF: 0.000295 AC: 45AN: 152324Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 04, 2021 | The c.139T>C (p.S47P) alteration is located in exon 4 (coding exon 4) of the C12orf75 gene. This alteration results from a T to C substitution at nucleotide position 139, causing the serine (S) at amino acid position 47 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at