chr17-1745347-G-A
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_000934.4(SERPINF2):c.117G>A(p.Pro39=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000062 in 1,612,864 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00015 ( 0 hom., cov: 28)
Exomes 𝑓: 0.000053 ( 0 hom. )
Consequence
SERPINF2
NM_000934.4 synonymous
NM_000934.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.449
Genes affected
SERPINF2 (HGNC:9075): (serpin family F member 2) This gene encodes a member of the serpin family of serine protease inhibitors. The protein is a major inhibitor of plasmin, which degrades fibrin and various other proteins. Consequently, the proper function of this gene has a major role in regulating the blood clotting pathway. Mutations in this gene result in alpha-2-plasmin inhibitor deficiency, which is characterized by severe hemorrhagic diathesis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 17-1745347-G-A is Benign according to our data. Variant chr17-1745347-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 710407.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.449 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINF2 | NM_000934.4 | c.117G>A | p.Pro39= | synonymous_variant | 4/10 | ENST00000453066.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINF2 | ENST00000453066.6 | c.117G>A | p.Pro39= | synonymous_variant | 4/10 | 5 | NM_000934.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 151554Hom.: 0 Cov.: 28
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GnomAD3 exomes AF: 0.0000479 AC: 12AN: 250620Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135798
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GnomAD4 exome AF: 0.0000527 AC: 77AN: 1461190Hom.: 0 Cov.: 43 AF XY: 0.0000578 AC XY: 42AN XY: 726900
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GnomAD4 genome AF: 0.000152 AC: 23AN: 151674Hom.: 0 Cov.: 28 AF XY: 0.000121 AC XY: 9AN XY: 74096
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 13, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at