chr11-57598295-A-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The NM_000062.3(SERPING1):c.25A>C(p.Thr9Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000307 in 1,562,280 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. T9T) has been classified as Likely benign.
Frequency
Consequence
NM_000062.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPING1 | NM_000062.3 | c.25A>C | p.Thr9Pro | missense_variant | 2/8 | ENST00000278407.9 | |
SERPING1 | NM_001032295.2 | c.25A>C | p.Thr9Pro | missense_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPING1 | ENST00000278407.9 | c.25A>C | p.Thr9Pro | missense_variant | 2/8 | 1 | NM_000062.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00144 AC: 217AN: 150952Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000355 AC: 60AN: 168948Hom.: 0 AF XY: 0.000264 AC XY: 24AN XY: 90884
GnomAD4 exome AF: 0.000186 AC: 263AN: 1411210Hom.: 2 Cov.: 32 AF XY: 0.000184 AC XY: 128AN XY: 697428
GnomAD4 genome ? AF: 0.00144 AC: 217AN: 151070Hom.: 0 Cov.: 31 AF XY: 0.00153 AC XY: 113AN XY: 73762
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at