Variant 17-1745973-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000934.4(SERPINF2):c.367+64A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 1,555,044 control chromosomes in the GnomAD database, including 425,846 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.73 ( 40494 hom., cov: 31)

Exomes 𝑓: 0.74 ( 385352 hom. )

Consequence

SERPINF2
NM_000934.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.679

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP6

Variant 17-1745973-A-G is Benign according to our data. Variant chr17-1745973-A-G is described in ClinVar as [Benign]. Clinvar id is 1282784.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 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.367+64A>G		intron_variant		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.367+64A>G		intron_variant		5	NM_000934.4	ENSP00000402286	P1	P08697-1

Frequencies

GnomAD3 genomes

AF:

0.730

AC:

110868

AN:

151892

Hom.:

40452

Cov.:

show subpopulations

Gnomad AFR

AF:

0.714

Gnomad AMI

AF:

0.813

Gnomad AMR

AF:

0.705

Gnomad ASJ

AF:

0.662

Gnomad EAS

AF:

0.855

Gnomad SAS

AF:

0.763

Gnomad FIN

AF:

0.738

Gnomad MID

AF:

0.633

Gnomad NFE

AF:

0.736

Gnomad OTH

AF:

0.710

GnomAD4 exome

AF:

0.740

AC:

1038843

AN:

1403034

Hom.:

385352

AF XY:

0.741

AC XY:

519555

AN XY:

701280

show subpopulations

Gnomad4 AFR exome

AF:

0.713

Gnomad4 AMR exome

AF:

0.693

Gnomad4 ASJ exome

AF:

0.662

Gnomad4 EAS exome

AF:

0.859

Gnomad4 SAS exome

AF:

0.768

Gnomad4 FIN exome

AF:

0.740

Gnomad4 NFE exome

AF:

0.739

Gnomad4 OTH exome

AF:

0.737

GnomAD4 genome

AF:

0.730

AC:

110965

AN:

152010

Hom.:

40494

Cov.:

AF XY:

0.730

AC XY:

54196

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.714

Gnomad4 AMR

AF:

0.705

Gnomad4 ASJ

AF:

0.662

Gnomad4 EAS

AF:

0.855

Gnomad4 SAS

AF:

0.761

Gnomad4 FIN

AF:

0.738

Gnomad4 NFE

AF:

0.736

Gnomad4 OTH

AF:

0.713

Alfa

AF:

0.676

Hom.:

2839

Bravo

AF:

0.725

Asia WGS

AF:

0.824

AC:

2864

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

DANN

Benign

0.65

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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