chr15-50471748-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005154.5(USP8):c.802T>A(p.Leu268Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0211 in 1,614,050 control chromosomes in the GnomAD database, including 433 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L268V) has been classified as Uncertain significance.
Frequency
Consequence
NM_005154.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP8 | NM_005154.5 | c.802T>A | p.Leu268Ile | missense_variant | 8/20 | ENST00000307179.9 | |
USP8 | NM_001128610.3 | c.802T>A | p.Leu268Ile | missense_variant | 8/20 | ||
USP8 | NM_001283049.2 | c.571T>A | p.Leu191Ile | missense_variant | 6/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP8 | ENST00000307179.9 | c.802T>A | p.Leu268Ile | missense_variant | 8/20 | 1 | NM_005154.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0164 AC: 2491AN: 152156Hom.: 25 Cov.: 32
GnomAD3 exomes AF: 0.0160 AC: 4011AN: 251216Hom.: 53 AF XY: 0.0167 AC XY: 2272AN XY: 135774
GnomAD4 exome AF: 0.0216 AC: 31566AN: 1461776Hom.: 408 Cov.: 31 AF XY: 0.0212 AC XY: 15406AN XY: 727190
GnomAD4 genome AF: 0.0164 AC: 2492AN: 152274Hom.: 25 Cov.: 32 AF XY: 0.0155 AC XY: 1154AN XY: 74466
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at