chr8-142741803-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PP3_ModeratePP5_Moderate
The NM_020427.3(SLURP1):c.178G>A(p.Glu60Lys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,611,402 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_020427.3 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLURP1 | NM_020427.3 | c.178G>A | p.Glu60Lys | missense_variant, splice_region_variant | 2/3 | ENST00000246515.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLURP1 | ENST00000246515.2 | c.178G>A | p.Glu60Lys | missense_variant, splice_region_variant | 2/3 | 1 | NM_020427.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000927 AC: 23AN: 248232Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 134732
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1459158Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 725946
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74376
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at