rs1057355
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000934.4(SERPINF2):c.*71G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000356 in 1,404,718 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 29)
Exomes 𝑓: 0.0000036 ( 0 hom. )
Consequence
SERPINF2
NM_000934.4 3_prime_UTR
NM_000934.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.355
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 Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINF2 | NM_000934.4 | c.*71G>A | 3_prime_UTR_variant | 10/10 | ENST00000453066.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINF2 | ENST00000453066.6 | c.*71G>A | 3_prime_UTR_variant | 10/10 | 5 | NM_000934.4 | P1 | ||
SERPINF2 | ENST00000382061.5 | c.*71G>A | 3_prime_UTR_variant | 10/10 | 1 | P1 | |||
SERPINF2 | ENST00000324015.7 | c.*71G>A | 3_prime_UTR_variant | 10/10 | 5 | P1 | |||
SERPINF2 | ENST00000450523.6 | c.*71G>A | 3_prime_UTR_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 29
GnomAD3 genomes
?
Cov.:
29
GnomAD4 exome AF: 0.00000356 AC: 5AN: 1404718Hom.: 0 Cov.: 29 AF XY: 0.00000573 AC XY: 4AN XY: 697806
GnomAD4 exome
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AC:
5
AN:
1404718
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Cov.:
29
AF XY:
AC XY:
4
AN XY:
697806
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 29
GnomAD4 genome
?
Cov.:
29
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at