Variant chr17-1762036-C-A 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 ENST00000571360.5(SERPINF1):c.-86C>A variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.0647 in 152,520 control chromosomes in the GnomAD database, including 521 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.065 ( 520 hom., cov: 33)

Exomes 𝑓: 0.041 ( 1 hom. )

Consequence

SERPINF1
ENST00000571360.5 5_prime_UTR

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 4.13

Variant links:

Genes affected

SERPINF1 (HGNC:8824): (serpin family F member 1) This gene encodes a member of the serpin family that does not display the serine protease inhibitory activity shown by many of the other serpin proteins. The encoded protein is secreted and strongly inhibits angiogenesis. In addition, this protein is a neurotrophic factor involved in neuronal differentiation in retinoblastoma cells. Mutations in this gene were found in individuals with osteogenesis imperfecta, type VI. [provided by RefSeq, Aug 2016]

SERPINF1 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=-0.53).

BP6

Variant 17-1762036-C-A is Benign according to our data. Variant chr17-1762036-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 321997.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-1762036-C-A is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SERPINF1	NM_002615.7 linkuse as main transcript			upstream_gene_variant		ENST00000254722.9	NP_002606.3
SERPINF1	NM_001329904.2 linkuse as main transcript			upstream_gene_variant			NP_001316833.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SERPINF1	ENST00000254722.9 linkuse as main transcript			upstream_gene_variant		1	NM_002615.7	ENSP00000254722	P1

Frequencies

GnomAD3 genomes

AF:

0.0646

AC:

9832

AN:

152160

Hom.:

517

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.108

Gnomad ASJ

AF:

0.0530

Gnomad EAS

AF:

0.0923

Gnomad SAS

AF:

0.0161

Gnomad FIN

AF:

0.0197

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0217

Gnomad OTH

AF:

0.0636

GnomAD4 exome

AF:

0.0413

AC:

AN:

242

Hom.:

Cov.:

AF XY:

0.0274

AC XY:

AN XY:

146

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.154

Gnomad4 FIN exome

AF:

0.0417

Gnomad4 NFE exome

AF:

0.0250

Gnomad4 OTH exome

AF:

0.0714

GnomAD4 genome

AF:

0.0647

AC:

9855

AN:

152278

Hom.:

520

Cov.:

AF XY:

0.0651

AC XY:

4850

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.135

Gnomad4 AMR

AF:

0.109

Gnomad4 ASJ

AF:

0.0530

Gnomad4 EAS

AF:

0.0921

Gnomad4 SAS

AF:

0.0159

Gnomad4 FIN

AF:

0.0197

Gnomad4 NFE

AF:

0.0217

Gnomad4 OTH

AF:

0.0643

Alfa

AF:

0.0486

Hom.:

120

Bravo

AF:

0.0749

Asia WGS

AF:

0.0530

AC:

184

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 16, 2021	This variant is associated with the following publications: (PMID: 16086313) -

Osteogenesis imperfecta

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

Aug 09, 2021

- -

Osteogenesis Imperfecta, Recessive

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

DANN

Benign

0.84

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