chr1-180166566-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002826.5(QSOX1):āc.341A>Gā(p.Asn114Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0031 in 1,614,066 control chromosomes in the GnomAD database, including 135 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002826.5 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 |
---|---|---|---|---|---|---|---|
QSOX1 | NM_002826.5 | c.341A>G | p.Asn114Ser | missense_variant | 2/12 | ENST00000367602.8 | |
QSOX1 | NM_001004128.3 | c.341A>G | p.Asn114Ser | missense_variant | 2/13 | ||
QSOX1 | XM_047426230.1 | c.341A>G | p.Asn114Ser | missense_variant | 2/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
QSOX1 | ENST00000367602.8 | c.341A>G | p.Asn114Ser | missense_variant | 2/12 | 1 | NM_002826.5 | P2 | |
QSOX1 | ENST00000367600.5 | c.341A>G | p.Asn114Ser | missense_variant | 2/13 | 1 | A2 | ||
QSOX1 | ENST00000392029.6 | c.341A>G | p.Asn114Ser | missense_variant, NMD_transcript_variant | 2/8 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0158 AC: 2402AN: 152158Hom.: 78 Cov.: 33
GnomAD3 exomes AF: 0.00422 AC: 1061AN: 251300Hom.: 29 AF XY: 0.00288 AC XY: 391AN XY: 135870
GnomAD4 exome AF: 0.00178 AC: 2598AN: 1461790Hom.: 57 Cov.: 31 AF XY: 0.00150 AC XY: 1094AN XY: 727206
GnomAD4 genome AF: 0.0158 AC: 2413AN: 152276Hom.: 78 Cov.: 33 AF XY: 0.0149 AC XY: 1108AN XY: 74464
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at