6-89146295-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001010853.3(PM20D2):c.151C>G(p.Leu51Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000215 in 1,581,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L51Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001010853.3 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 |
---|---|---|---|---|---|---|---|
PM20D2 | NM_001010853.3 | c.151C>G | p.Leu51Val | missense_variant | 1/7 | ENST00000275072.5 | |
LOC101929004 | XR_942766.4 | n.572G>C | non_coding_transcript_exon_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PM20D2 | ENST00000275072.5 | c.151C>G | p.Leu51Val | missense_variant | 1/7 | 1 | NM_001010853.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000784 AC: 15AN: 191362Hom.: 0 AF XY: 0.0000654 AC XY: 7AN XY: 107056
GnomAD4 exome AF: 0.0000210 AC: 30AN: 1428922Hom.: 0 Cov.: 31 AF XY: 0.0000211 AC XY: 15AN XY: 709926
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2023 | The c.151C>G (p.L51V) alteration is located in exon 1 (coding exon 1) of the PM20D2 gene. This alteration results from a C to G substitution at nucleotide position 151, causing the leucine (L) at amino acid position 51 to be replaced by a valine (V). 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