chr6-27309877-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033482.4(POM121L2):c.2294C>T(p.Pro765Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000425 in 1,551,660 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033482.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POM121L2 | NM_033482.4 | c.2294C>T | p.Pro765Leu | missense_variant | 1/1 | ENST00000444565.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POM121L2 | ENST00000444565.2 | c.2294C>T | p.Pro765Leu | missense_variant | 1/1 | NM_033482.4 | P1 | ||
POM121L2 | ENST00000429945.1 | c.216+1220C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000510 AC: 8AN: 156874Hom.: 0 AF XY: 0.0000361 AC XY: 3AN XY: 83022
GnomAD4 exome AF: 0.0000336 AC: 47AN: 1399432Hom.: 0 Cov.: 63 AF XY: 0.0000304 AC XY: 21AN XY: 690216
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 22, 2023 | The c.2294C>T (p.P765L) alteration is located in exon 1 (coding exon 1) of the POM121L2 gene. This alteration results from a C to T substitution at nucleotide position 2294, causing the proline (P) at amino acid position 765 to be replaced by a leucine (L). 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