chr1-180154924-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002826.5(QSOX1):c.17G>T(p.Ser6Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,466,162 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002826.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
QSOX1 | NM_002826.5 | c.17G>T | p.Ser6Ile | missense_variant | 1/12 | ENST00000367602.8 | |
QSOX1 | NM_001004128.3 | c.17G>T | p.Ser6Ile | missense_variant | 1/13 | ||
QSOX1 | XM_047426230.1 | c.17G>T | p.Ser6Ile | missense_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
QSOX1 | ENST00000367602.8 | c.17G>T | p.Ser6Ile | missense_variant | 1/12 | 1 | NM_002826.5 | P2 | |
QSOX1 | ENST00000367600.5 | c.17G>T | p.Ser6Ile | missense_variant | 1/13 | 1 | A2 | ||
QSOX1 | ENST00000392029.6 | c.17G>T | p.Ser6Ile | missense_variant, NMD_transcript_variant | 1/8 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152070Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000300 AC: 2AN: 66746Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 37742
GnomAD4 exome AF: 0.0000114 AC: 15AN: 1313984Hom.: 0 Cov.: 30 AF XY: 0.00000465 AC XY: 3AN XY: 645668
GnomAD4 genome AF: 0.000105 AC: 16AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74404
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at