rs200534715
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_000062.3(SERPING1):āc.352A>Gā(p.Thr118Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000981 in 1,498,686 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_000062.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPING1 | NM_000062.3 | c.352A>G | p.Thr118Ala | missense_variant | 3/8 | ENST00000278407.9 | |
SERPING1 | NM_001032295.2 | c.352A>G | p.Thr118Ala | missense_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPING1 | ENST00000278407.9 | c.352A>G | p.Thr118Ala | missense_variant | 3/8 | 1 | NM_000062.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000372 AC: 5AN: 134576Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000227 AC: 57AN: 251392Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135870
GnomAD4 exome AF: 0.000104 AC: 142AN: 1364012Hom.: 0 Cov.: 39 AF XY: 0.000103 AC XY: 70AN XY: 678340
GnomAD4 genome ? AF: 0.0000371 AC: 5AN: 134674Hom.: 0 Cov.: 31 AF XY: 0.0000309 AC XY: 2AN XY: 64678
ClinVar
Submissions by phenotype
not provided Benign:1Other:1
not provided, no classification provided | literature only | UniProtKB/Swiss-Prot | - | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 16, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Hereditary angioedema type 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at