Variant rs35259159 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000934.4(SERPINF2):c.186C>T(p.Ala62=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0509 in 1,613,594 control chromosomes in the GnomAD database, including 2,557 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.039 ( 179 hom., cov: 31)

Exomes 𝑓: 0.052 ( 2378 hom. )

Consequence

SERPINF2
NM_000934.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.289

Variant links:

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]

SERPINF2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 17-1745728-C-T is Benign according to our data. Variant chr17-1745728-C-T is described in ClinVar as [Benign]. Clinvar id is 256835.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.289 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SERPINF2	NM_000934.4 linkuse as main transcript	c.186C>T	p.Ala62=	synonymous_variant	5/10	ENST00000453066.6	NP_000925.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SERPINF2	ENST00000453066.6 linkuse as main transcript	c.186C>T	p.Ala62=	synonymous_variant	5/10	5	NM_000934.4	ENSP00000402286	P1	P08697-1

Frequencies

GnomAD3 genomes

AF:

0.0389

AC:

5919

AN:

152072

Hom.:

179

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0105

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.0346

Gnomad ASJ

AF:

0.00634

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00311

Gnomad FIN

AF:

0.0476

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0634

Gnomad OTH

AF:

0.0378

GnomAD3 exomes

AF:

0.0389

AC:

9736

AN:

250460

Hom.:

272

AF XY:

0.0387

AC XY:

5245

AN XY:

135484

show subpopulations

Gnomad AFR exome

AF:

0.00974

Gnomad AMR exome

AF:

0.0221

Gnomad ASJ exome

AF:

0.00527

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00506

Gnomad FIN exome

AF:

0.0507

Gnomad NFE exome

AF:

0.0643

Gnomad OTH exome

AF:

0.0414

GnomAD4 exome

AF:

0.0521

AC:

76208

AN:

1461404

Hom.:

2378

Cov.:

AF XY:

0.0508

AC XY:

36965

AN XY:

726984

show subpopulations

Gnomad4 AFR exome

AF:

0.00675

Gnomad4 AMR exome

AF:

0.0250

Gnomad4 ASJ exome

AF:

0.00635

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00490

Gnomad4 FIN exome

AF:

0.0547

Gnomad4 NFE exome

AF:

0.0617

Gnomad4 OTH exome

AF:

0.0436

GnomAD4 genome

AF:

0.0389

AC:

5920

AN:

152190

Hom.:

179

Cov.:

AF XY:

0.0359

AC XY:

2674

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.0105

Gnomad4 AMR

AF:

0.0346

Gnomad4 ASJ

AF:

0.00634

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00311

Gnomad4 FIN

AF:

0.0476

Gnomad4 NFE

AF:

0.0634

Gnomad4 OTH

AF:

0.0374

Alfa

AF:

0.0493

Hom.:

107

Bravo

AF:

0.0368

Asia WGS

AF:

0.00520

AC:

AN:

3478

EpiCase

AF:

0.0568

EpiControl

AF:

0.0596

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

3.6

DANN

Benign

0.40

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over