20-1125500-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_006814.5(PSMF1):c.132G>A(p.Pro44Pro) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000891 in 1,605,752 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_006814.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PSMF1 | NM_006814.5 | c.132G>A | p.Pro44Pro | splice_region_variant, synonymous_variant | 2/7 | ENST00000335877.11 | NP_006805.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PSMF1 | ENST00000335877.11 | c.132G>A | p.Pro44Pro | splice_region_variant, synonymous_variant | 2/7 | 1 | NM_006814.5 | ENSP00000338039.6 |
Frequencies
GnomAD3 genomes AF: 0.00373 AC: 567AN: 152140Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00119 AC: 290AN: 243506Hom.: 3 AF XY: 0.000843 AC XY: 111AN XY: 131666
GnomAD4 exome AF: 0.000595 AC: 865AN: 1453494Hom.: 3 Cov.: 30 AF XY: 0.000510 AC XY: 369AN XY: 722990
GnomAD4 genome AF: 0.00372 AC: 566AN: 152258Hom.: 4 Cov.: 32 AF XY: 0.00360 AC XY: 268AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 24, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at