chr20-1135221-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_006814.5(PSMF1):c.466C>T(p.Arg156Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000219 in 1,614,130 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R156Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_006814.5 missense
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 | UniProt |
---|---|---|---|---|---|---|---|
PSMF1 | NM_006814.5 | c.466C>T | p.Arg156Trp | missense_variant | 4/7 | ENST00000335877.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSMF1 | ENST00000335877.11 | c.466C>T | p.Arg156Trp | missense_variant | 4/7 | 1 | NM_006814.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00122 AC: 186AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000290 AC: 73AN: 251434Hom.: 0 AF XY: 0.000235 AC XY: 32AN XY: 135894
GnomAD4 exome AF: 0.000114 AC: 166AN: 1461868Hom.: 2 Cov.: 31 AF XY: 0.000109 AC XY: 79AN XY: 727236
GnomAD4 genome ? AF: 0.00123 AC: 188AN: 152262Hom.: 0 Cov.: 32 AF XY: 0.00116 AC XY: 86AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 24, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at