chr14-94290332-G-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001100607.3(SERPINA10):c.262C>T(p.Arg88*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00645 in 1,614,230 control chromosomes in the GnomAD database, including 84 homozygotes. Variant has been reported in ClinVar as Likely benign (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001100607.3 stop_gained
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SERPINA10 | NM_001100607.3 | c.262C>T | p.Arg88* | stop_gained | Exon 2 of 5 | ENST00000261994.9 | NP_001094077.1 | |
SERPINA10 | NM_016186.3 | c.262C>T | p.Arg88* | stop_gained | Exon 2 of 5 | NP_057270.1 | ||
SERPINA10 | XM_017021353.2 | c.382C>T | p.Arg128* | stop_gained | Exon 3 of 6 | XP_016876842.1 | ||
SERPINA10 | XM_005267733.6 | c.262C>T | p.Arg88* | stop_gained | Exon 2 of 5 | XP_005267790.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SERPINA10 | ENST00000261994.9 | c.262C>T | p.Arg88* | stop_gained | Exon 2 of 5 | 1 | NM_001100607.3 | ENSP00000261994.4 | ||
SERPINA10 | ENST00000554723.5 | c.382C>T | p.Arg128* | stop_gained | Exon 2 of 5 | 1 | ENSP00000450896.1 | |||
SERPINA10 | ENST00000393096.5 | c.262C>T | p.Arg88* | stop_gained | Exon 2 of 5 | 1 | ENSP00000376809.1 | |||
SERPINA10 | ENST00000554173.1 | c.262C>T | p.Arg88* | stop_gained | Exon 1 of 4 | 1 | ENSP00000450971.1 |
Frequencies
GnomAD3 genomes AF: 0.00532 AC: 810AN: 152228Hom.: 8 Cov.: 33
GnomAD3 exomes AF: 0.00718 AC: 1802AN: 251086Hom.: 13 AF XY: 0.00797 AC XY: 1081AN XY: 135716
GnomAD4 exome AF: 0.00657 AC: 9604AN: 1461884Hom.: 78 Cov.: 37 AF XY: 0.00702 AC XY: 5105AN XY: 727242
GnomAD4 genome AF: 0.00530 AC: 808AN: 152346Hom.: 6 Cov.: 33 AF XY: 0.00554 AC XY: 413AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:1
- -
LAMB2-related infantile-onset nephrotic syndrome Benign:1
The heterozygous p.Arg88Ter variant in SERPINA10 has been identified in 3 individuals with venous thromboembolic disease, including an individual with Factor V Leiden, and 1 homozygous individual with autism spectrum disorder (PMID: 15461625, 22039093, 23352160), and has been identified in >1% of South Asian chromosomes and 6 homozygotes by ExAC (http://gnomad.broadinstitute.org/). A meta-analysis suggests this variant does not cause increased risk of disease (PMID: 18710385). In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely benign for autosomal dominant venous thromboembolic disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at